Lockyer, who sat the game out due to a shattered left cheekbone, finishes a glittering career for the Broncos on 355 games and four premierships and was sorely missed by his team.
A litany of soft penalties really hurt the Broncos as a pair of tries from William Hopoate, four-pointers from Matt Ballin, Brett Stewart and Kieran Foran and three goals from Jamie Lyon sealed the victory in front of a crowd of 31,894.
Boosted by the extra week off, the Sea Eagles came racing out of the blocks and opened the scoring in the fourth minute through Ballin.
The Broncos conceded two soft penalties allowing Manly to march their way down the field and the hooker dived over from dummy-half to give his side the perfect start.
From the resulting kick-off the visitors almost hit back immediately when Corey Parker's restart cannoned off the crossbar and was regathered by Peter Wallace in front of the posts.
However, Manly held firm in defence to usher Yow Yeh into touch to snuff out the danger.
Jack Reed then went close to grabbing his side's first try of the night when he hauled in Matt Gillett's kick, only for teammate Dale Copley to knock the ball out of his hands and the chance went begging.
That setback appeared to knock the stuffing out the young Broncos, and Copley then capped off a nightmare 60 seconds when he misread a pass from Reed in front of his own posts.
The ever-alert Daly Cherry-Evans latched onto the loose ball and teed up Will Hopoate who scored his easiest try of a superb season.
Things got worse for Anthony Griffin's side in the 21st minute when Manly stretched their advantage through Stewart's try following a sharp pass from Cherry-Evans.
The visitors had the last word of the half when Yow Yeh produced a stunning take from a Gillett bomb, leaping over Michael Robertson before twisting in mid-air to ground the ball over the line.
The Sea Eagles started the second half in similar fashion when Hopoate dived over for his second seven minutes after the restart.
The Broncos hit back when Wallace bulldozed his way over from close range 10 minutes later, only for Foran to seal the game on the hour-mark when he got in front of Gerard Beale to grab a Cherry-Evans kick and score near the posts with Lyon adding the extras.
Griffin's side battled well until the end and Gillett was denied a try 10 minutes from time by an amazing tackle from Lyon, before Copley added some respectability to the scoring with a try in the corner late in the game.
Key moment: Sea Eagles five-eighth Kieran Foran brilliantly grabs a towering Daly Cherry-Evans bomb and dives over to score, making it 26-10 and snuffing out the hint of a Broncos comeback.
Man of the match: Manly halfback Daly Cherry-Evans. Had a hand in four of his side's five tries as his boom year just gets bigger.
Injuries: Jharal Yow Yeh (ribs)
Judiciary: Big trouble for Manly. Backrower Tony Williams on report for a blatant 63rd minute high shot on Broncos winger Jharal Yow Yeh. And serial offender Steve Matai for leading with the knees in a tackle on a luckless Yow-Yeh two minutes later.
What's next: Manly move into a first grand final since their premiership of 2008. They will play arch rivals Melbourne or the Warriors on Sunday, October 2 at ANZ Stadium. The NRL career of Brisbane great and Test captain Darren Lockyer is over.
- AAP
