Dismay turned to anger when Krishna opened the scoring in additional time, twisting in the penalty area before lashing a right foot shot past Phil Imray.
That moment proved to be a turning point in the match.
In the second half, Waitakere squeezed Wellington out of the match with their more experienced outfit took control of midfield.
Where Wellington had created chances with regularity in the first half, they were left to feed on scraps in the second with Lucas working hard to create chances without success.
The match drifted away from the visitors with 13 minutes left when Pearce lashed home Waitakere's second, before Butler sealed the result with five minutes remaining.
Wellington responded within 60 seconds, with Henry Fa'arodo's near post header giving the Matt Calcott-coached side the faintest of hope, but Krishna put the match to bed when he notched his second with a minute left to play.
The result capped a roller-coaster season for the Neil Emblen-led champions, who at one stage looked odds on to not only lose their title but miss out on O-League football for the first time since the competition was established in 2006-07 season.
"I think there's a little bit of know-how in our group, the players know what's at stake," Emblen said. "Tonight's performance wasn't a vintage performance, and we had to dig in and show a bit of character in the first half against a good team that outplayed us."
Defeat broke Wellington hearts, missing out on a first ASB Premiership title and a maiden taste of O-League football. It was also Wellington's second grand final defeat in four years to the same opponents.
Calcott was adamant the Bale-Lucas decision in time added on at the end of the first half was a pivotal moment.
"I thought it was crucial - it looked contentious to me," he said. "They went up the other end and they scored. Key moments in a game like that can change things. I thought we were excellent in the first half and if we had got a wee goal ahead and that would've changed the look of the game.
"But Waitakere were good in the second half and thoroughly deserved their victory."