The Panthers hit back with their first try of the match soon after the break, with Malakai Watene-Zelezniak crossing out wide.
The six-point margin could have been further reduced but Nathan Cleary's conversion attempt was wide and also came after the 30 second time limit expired.
The Roosters soon resumed their attack down the other end of the field but a knock-on over the try line kept the score at 10-4.
With less than two minutes remaining the Panthers stunned the Roosters with a long-range try to Cleary but the conversion was again waved away.
Roosters youngster Conor Watson was awarded with the Player of the Tournament medal post-match.
6.50pm - Roosters dominating Panthers
The Roosters started the final with a flurry of attacking play that saw Kiwi-born flyer Joseph Manu come close to scoring on the right side only to be denied by strong defence.
They opened their account soon after, with wing Daniel Tupou scoring to help the Roosters establish a 6-0 lead after three minutes.
They were in again soon after following a knock-on from Penrith, with Bernard Lewis diving in to the opposite corner to extend their lead to 10-0.
The Panthers were unable to get into the match with the Roosters then forcing a line drop-out to further dominate possession and territory before the break.
5.25pm - Panthers to face Roosters in tournament decider
The Sydney Roosters are through to the decider after Bernard Lewis scored a last minute runaway try to upset the Storm 21-16.
5pm - Panthers too strong for Eels
Penrith are through to the tournament final after dispatching Parramatta 13-0 in the first semi final.
Waqa Blake scored the first of two tries in a tight first half that saw them lead 4-0 at the break, before a four-pointer to Malaki Watene-Zelezniak extended the lead, with Blake's second securing victory.
They await the outcome of the second semi final between the Storm and Roosters to see who they will face in the decider.
Earlier, the Kiwi Ferns lost 8-0 to the Jillaroos in the second transtasman women's clash, with a third game to follow the last semi.
4.11pm - Cowboys skipper Johnathan Thurston slams poor crowd turnout
North Queensland star Johnathan Thurston has slammed the poor crowd turnout at Eden Park and joined the chorus of NRL figures saying the tournament needs to leave Auckland.
Speaking after the Cowboys shock 25-12 quarter final loss to Melbourne, Thurston said he enjoyed his debut Nines campaign but felt the event could be more successful if it was moved to another city or country.
"It's a great way to kick off the year, playing in the Nines," he said. (But) I'm pretty disappointed at the turn-out of the crowd.
"If that's the type of crowd that's going to show up I reckon we should be taking it elsewhere.
"Maybe even Asia, get over there for a week and try and grow the game."
Thurston was full of praise for the nature of the shois a b festivities and felt it had great appeal for spectators.
However, the Kangaroos and Queensland playmaker believes Auckland league fans don't deserve to have the Nines in their own backyard if they aren't going to turn out in force to support the concept.
"You can see it's a great spectacle and if its going get a turnout like this then lets take it elsewhere," he said.
"It's a great weekend. The fans love it, the players really enjoy it.
"It's only my first experience. I had a lot of fun. We got beaten by a better side today so that's the way footy goes.
"But I think we can grow it elsewhere."
3.53pm - Roosters and Storm advance
Surprise quarter final results mean the Sydney Roosters will meet Melbourne Storm to fight for a place in the tournament decider.
The plucky Roosters edged the Brisbane Broncos 15-14 in a match that ended in controversy after Broncos and Kiwis test star Jordan Kahu's conversion was denied when he kicked the ball as the fulltime siren blew.
Meanwhile, the youthful Storm side ended the Cowboys unbeaten run with an impressive 25-12 win to book their place in the final.
The Panthers and Eels will contest the first semi-final at 4.40pm.
The crowd is currently enjoying the second transtasman test between the Kiwi Ferns women's side against the Australian Jillaroos, after the visitors claimed a first-up 20-4 win yesterday.
3.10pm - Nines should move from Auckland, says Shaun Johnson
Warriors star Shaun Johnson's groin injury is not serious but he was not prepared to risk sustaining further damage by playing at the NRL Auckland Nines.
Johnson was today ruled out of playing on day two of the Eden Park tournament after missing their first two games yesterday when the injury flared up during the team's warm-up.
The 26-year-old is disappointed at not being able to play in the tournament that has become synonymous with his name over the past four years, but the injury was affecting his running speed and he felt it would affect his performance.
"Obviously it wasn't what we had in mind," Johnson told Newstalk ZB's Tony Veitch.
"I had a set-back ahead of our first game, I pulled up a bit lame in the warm-up and with that change the boys went out and did the best they could.
"To be fair we had a pretty young side out there. They tried their hardest all weekend and played against a couple of very good sides. It wasn't meant to be this year."
Johnson is not expected to be out of action for long and remains a chance of playing in the Warriors NRL trial games against Melbourne Storm and the Gold Coast Titans in the next two weeks.
The Kiwis test halfback is no stranger to playing with injury and admits he may have taken the field if it was an important NRL game vital to the Warriors playoff hopes.
However, he was not prepared to risk suffering further damage this early in the preseason.
"I've played the bulk of last seasons with similar sort of niggles but I don't think I would have played with this one," he said.
"It is just that top-end speed stuff where it really grabs.
"Who knows? With different circumstances maybe, but definitely at this point of the year, I didn't feel I could go out there and deliver a performance I would be happy with, carrying that injury. So that's why I made the call.
"I wanted to be out there as much as I could but at the same time I have to listen to our club staff."
In assessing the future of the Nines, Johnson was in agreement with Warriors managing director Jim Doyle in believing the event needs to move out of Auckland and be rotated through different cities each year.
He hoped that would enable Kiwi league fans to still look forward to attending the Nines but felt the event could benefit by being introduced to a fresh audience.
"I think it is time to move it on and create that buzz again to another city.
"It definitely has to come back to Auckland though. You can't just take it away and play it in Brisbane or Melbourne for five years.
"You've got to be able to rotate it and know if you're in Auckland or New Zealand that the Nines will be back in a few years."
2.50pm Eels remain on course to defend title
Parramatta remain on course to repeat their 2016 truimph at the Auckland Nines, after a 14-0 over the Titans in the second quarter final on Sunday.
The Eels were the dominant side throughout while the Gold Coast team struggled without the injured Jarryd Hayne.
The Eels face the Panthers in the first semi final.
The next quarter final is between the Broncos and Roosters, followed by the Cowboys clash with the Storm.
2.15pm Penrith into semi finals after thriller
Penrith are into the semi finals of the NRL Nines, after a thrilling 16-12 over Manly.
After the match went to extra time - with the teams tied 12-12 - utility Tyrone May crashed over in the second minute of the extra period.
The Panthers progress is ironic, as the west Sydney club have been one of the most outspoken critics of the tournament.
CEO Phil Gould has been constantly negative about the event and their chairman said last week that the Nines carried too much of an injury risk.
1:20pm Shaun Johnson injury 'not serious'
Shaun Johnson is likely to feature in the club's pre-season programme of trials, which begin next week against the Melbourne Storm.
While the halfback took no part in their failed Nines campaign as he was sidelined by a hip complaint, Warriors assistant coach Steve Mac Namara said he expected Johnson to be involved over the next fortnight.
"I don't think it's serious," said MacNamara. "Hopefully he'll be ok for trial one next week if not definitely trial two the week after."
MacNamara said the decision not to play Johnson on the final day of the Nines was made on Sunday morning.
"We gave him every chance but it simply wasn't worth the risk of putting Shaun out there for this game."
"[He was] hugely disappointed," said MacNamara. "He's a proud man and really likes this tournament and likes to get out there and show what he can do but unfortunately he wasn't able to. It was in the club's best interests that he didn't play."
Meanwhile, the final games in the Hunua pool saw the Tigers beat the Broncos 17-11and the Storm trump the Knights 20-10
12:25pm Warriors end Nines winless
The Warriors woe's have continued on Sunday at the Nines, with a last minute 14-10 loss to the Dragons.
The match looked headed for a draw, before Kurt Mann broke through from 30 metres out to dot down with less than 30 seconds left on the clock.
It means the Warriors have failed to win a single match at this year's tournament, which is a poor effort.
Though they were fielding a young team, they should have been good enough to beat the Dragons, who have hardly any big names in their squad.
Just like yesterday the Warriors had their chances, but a lack of composure and basic errors let them down.
It wasn't good enough. Even young players should be able to make good decisions under pressure, but the sight of Sam Lisone putting in a hopeful left footed grubber kick midway through the first half hinted at panic in the ranks.
Earlier Ata Hingano had opened the scoring for the Warriors in the fifth minute, as the home team opened with an intensity that hasn't been apparent on Saturday.
But it didn't last. Nene MacDonald replied soon afterwards for the Sydney side, beating several would be tacklers to score a relatively soft try.
Tui Lolohea scored a solo effort - regathering his own chip - to put the Warriors ahead early in the second half, before St George again replied to tie up the match.
The Dragons had the better chances late in the match, with MacDonald losing the ball over the try line after making a long range break.
The Warriors looked disorganised and were playing far too lateral, though Lolohea also sparked a late break before Mann's fateful try.
In earlier matches on Sunday the Sharks thrashed a disinterested Bulldogs side 28-4, while the Panthers suprised the Titans 22-4.
In the battle for top spot in the Piha pool, 2016 champions Parramatta Eels beat Manly 17-12.
11.00am: Johnson unlikely to play
Shaun Johnson has no contractual obligation to take the field today.
Johnson is an ambassador of the Duco event, and one of the faces of the Nines.
He has been contracted in a separate deal to promote the event - like Johnathan Thurston - but the deal does not include any clauses related to his participation in the Nines.
While there was an expectation from the promoters that he would be part of the team and take the field, the ultimate decision rests with Warriors head coach Stephen Kearney and assistants Steve MacNamara and Stacey Jones, who are running the Nines team.
The halfback sat out both of the Warriors losses on Saturday, with the club saying he was struggling with a hip complaint.
It's unknown if the 26-year-old will take any part in their final match on Sunday against the Dragons.
With nothing riding on the result - as the Warriors are already eliminated from the tournament - it seems unlikely that the Warriors would risk him.
The Warriors' exit is likely to have an impact on the crowd and the atmosphere today, though there remains plenty of interest in Johnathan Thurston and the Cowboys, as well as other popular teams like the Broncos, Eels and Roosters.