Warriors halfback Te Maire Martin starred on return from a hamstring injury, before halves partner Chanel Harris-Tavita clinched the see-sawing affair with a field goal in the last three minutes.
The Warriors enter the finals series on a six-game winning streak, but they have a tenuous hold on first place heading into the last day of the regular season.
Playing at near full strength, the Panthers need only beat 15th-placed Wests Tigers by two points on Sunday to leapfrog the Warriors into first place.
That would leave the Kiwi club to host the third-placed Dolphins in the first week of finals, with the Sydney Roosters awaiting should they hold top spot.
More pressingly, the Warriors have conceded an average of 29.3 points across their last three games, with Manly exploiting their edge defence in Auckland on Saturday.
But Webster is remaining calm as the Warriors enter the finals with their most wins of any regular season in their 32-year history.
"I'm not stupid, I know we've got to clean some stuff up," he said.
"But I know what sort of week we had this week, I know how much better we're going to be for the run, I know we're going to build some confidence from it.
"We're in a good spot."
The result pulls the curtain down on a rollercoaster season for the Sea Eagles, who finish ninth with an 11-13 record, despite briefly sitting in the top four.
Manly will be left to rue the slow start to 2026 that cost Anthony Seibold his job, and a six-game losing streak that followed Luke Brooks' ACL injury.
The Sea Eagles also finish the season with four one-point losses; had they won all four, they would be hosting a home elimination final next weekend.
"That's the difference between being there and not being there," said coach Kieran Foran.
The Sea Eagles saved one of their gutsiest performances of 2026 for their first game since being officially eliminated from finals contention.
Manly did not play the ball in the Warriors' red zone until the 57th minute and needed to withstand a sin-binning to Ben Trbojevic (hip-drop tackle) right as the Warriors were humming.
But led by Tom Trbojevic, the Sea Eagles found success shifting the ball inside their own half as Lehi Hopoate and Reuben Garrick bagged two tries each.
Trbojevic was penalised for holding Jacob Laban ahead of a would-be a Clayton Faulalo try that could have put Manly up by 12 points with 15 minutes left.
Moments later, the Warriors equalised as fullback Taine Tuaupiki completed his hat-trick.
"It felt like not a lot went our way, but we were able to just keep fighting and stay in the game," Trbojevic said.
"Unlucky not to go 12 points up ... they go down and score, and then we're in a field-goal off and we just couldn't get it done, unfortunately."
The individual brilliance of Martin, five tries between Tuaupiki and Charnze Nicoll-Klokstad, and Harris-Tavita's one-pointer were enough to seal a Warriors victory.
Martin sent beautifully weighted passes to second-rowers Eddie Ieremia-Toeva and Jacob Laban ahead of the Warriors' first two tries.
He popped up a ball for Tuaupiki to cut inside and complete his double, then helped Nicoll-Klokstad do the same with a kick after the break.
Manly forward Caleb Navale charged down Harris-Tavita's first field goal attempt, before the five-eighth struck from directly in front in the final minutes.
