The Roar will now face second-placed Western Sydney Wanderers next weekend at Pirtek Stadium, and the winner will move through to the A-League grand final.
For Victory, their season is over.
A week on from frustrating the Roar out of Premiers' Plate contention in a scoreless stalemate at AAMI Park, they received a taste of their own medicine.
Melbourne completely bossed the first half, taking 10 shots to Brisbane's zero, but went into the break with nothing to show for it.
It seemed as if the occasion might have gotten to the Roar's usually slick midfield unit, which struggled to string together passes and repeatedly coughed up possession, with veteran Corona surprisingly the biggest culprit.
Victory's dominance continued into the second half, but a second yellow card to Jason Geria in the 83rd minute reduced them to 10 men and swung the momentum Brisbane's way.
But even after Berisha's goal, Aloisi said he still believed the Roar could win.
"It's the spirit of the club, the character of the players," he said.
"They've shown in the past and this season - we never give up, we go right to the end. "To do it again like that was brilliant for the fans and for the players."
Victory coach Kevin Muscat said he was "shattered" for his players.
"I don't think we deserved that tonight. We were very good," he said.
"We were the better team but it can be a cruel game sometimes and it's certainly one of those nights tonight.
"For the season to finish like it has for us tonight, I'm gutted."
-AAP