With the match deadlocked with eight minutes left on the clock, Roosters star Sonny Bill Williams appeared to drop the ball cold in a tackle.
The referees deemed otherwise, awarded the Roosters a penalty and, three minutes later, Maloney slotted the match-winning one-pointer.
"I don't think I've ever seen a footy game like that. I don't think I've ever coached in one like that," said Roosters coach Trent Robinson.
"I think we saw the best and worst of both teams tonight."
The premiers' heart-stopping win set up a blockbuster preliminary final with South Sydney next Friday night at ANZ Stadium.
James Maloney scores for the Roosters as they take a 30-0 lead in the first half. Photo / Getty Images
But a rematch three weeks after their minor premiership showdown with the Rabbitohs still wasn't certain even after Maloney nudged the Roosters back in front as the clock wound down.
In a helter skelter finish, Thurston had Roosters fans with their hearts in their mouths when he raced away to touch down in the final minute of the match, only to be denied the try when the video referees ruled a knock-on against Cowboys five-eighth Robert Lui in the lead-up.
Jonathan Thurston inspired the Cowboys' comeback. Photo / Getty Images
It was another bitter pill for the Cowboys to swallow after last year's infamous seventh-tackle try to Cronulla winger Beau Ryan ended their campaign.
The year before, the Cowboys were eliminated after Kieran Foran's so-called "Hand of God" allowed Manly a dubious try in another controversial finals finish.
This time, though, the Cowboys refused to cry foul, with both Thurston and coach Paul Green blaming the side's dreadful opening half hour - not any calls at the death - for their finals exit.
"At the end of the day, it was the start to the match that put us behind the eight-ball," Thurston said.
"I'm still filthy. It still hurts. It's a bitter pill to swallow."
James Maloney sets himself for a field goal that would prove to be the difference between the sides. Photo / Getty Images
On the rebound from their last-minute qualifying final loss to Penrith last Saturday night, the Roosters came out on fire on Friday night.
Maloney and halfback Mitchell Pearce gave the premiers a lightning start.
Pearce bolted 93 metres to score in just the third minute after snapping up an ill-directed kick from Cowboys fullback Michael Morgan, who had a night to forget.
After slotting the conversion, Maloney fired a superb cut-out pass to put winger Daniel Tupou over in the left-hand corner.
Maloney then had a hand or boot in the Roosters' third and fourth tries to Tupou and centre Michael Jennings before doing it all himself for the fifth that put the titleholders up 30-0.
But tries to forwards Ethan Lowe and Gavin Cooper, both converted by Thurston, gave the Cowboys hope when they went to the sheds trailing 30-12 at halftime.
When Thurston dummied his way over and converted shortly after the break, the Roosters' lead was suddenly cut to 12 points.
The Roosters' advantage was only six points after a terrible blunder from skipper Anthony Minichiello - playing his club-record-equalling 301st match - gifted Lui a try next to the posts.
The semi-final was anyone's after Test prop Matt Scott powered over to lock it all up at 30-30 - before Maloney had the final say.
-AAP
