The triumph, however, may have come at a significant cost, with Socceroo attacker Nishan Velupillay forced off at halftime with a potentially serious injury to his lower right leg.
Auckland coach Steve Corica, meanwhile, was left fuming about a "disgraceful decision" to rule out a goal that would have levelled the tie.
Velupillay emerged to watch the second half on crutches, with serious questions now hovering over his availability for crunch World Cup qualifiers against Japan and Saudi Arabia next month.
"It doesn't look good at the moment, he's in a bit of pain," Victory boss Arthur Diles said of Velupillay.
"So we'll wait till we get back to Melbourne and get him scanned and evaluated."
The vast majority of the 29,148 fans on hand were hoping to see the hosts become the first side in league history to secure a premiership and championship double in their first season.
They created a party-like atmosphere, only to be left stunned when two goals from Zinedine Machach and Bruno Fornaroli overturned the first-leg deficit in the space of five second-half minutes.
Taking a wicked deflection off Nando Pijnaker, Machach struck first in the 55th minute before a superb pass from Jordi Valadon found Fornaroli at the top of the box, allowing the Socceroos striker to masterfully turn and shoot ten minutes later.
"It was beautiful to play in front of 30,000 fans tonight," said Diles.
"It was even nicer to spoil the party."
In dramatic scenes, Logan Rogerson thought he levelled on aggregate when he headed in at the far post in the 69th minute, only for it to be ruled that Guillermo May's cross had gone out before swinging back onto his head, leaving Corica irate.
"We all saw the replay, the ball's in play," said the Auckland coach.
"The referee has made his bad decision, the linesman has, and so has the VAR.
"That would have helped us get back into the game."
The hosts hurled everything they had at the Victory as time wound down but their desperate attempts proved in vain, with Josh Rawlins clearing a Pijnaker effort off the line 98th minute to seal back-to-back grand final appearances.
"It's a great moment for us as a football club, something we've worked really hard for," said Diles.
"And you get a reward tonight off the back of that."
