With only three minutes to play in regulation time on Saturday night, substitute Nicolas Milanovic put the Wanderers on course for their comeback win with a left-foot strike from the edge of the box.
It was the 23-year-old's ninth goal of a great season, with CommBank Stadium erupting as the hosts took an unlikely 3-2 lead.
Swedish veteran Marcus Antonsson iced the result loping into the box on a counterattack to seal an emphatic win in added time.
Western Sydney had trailed 2-0 just before halftime but will now finish the weekend in third place on the ladder and are undefeated in their past six games.
"People didn't believe me when I said early on in press conferences, that I'd seen our team play in pre-season and I had enough belief that we could win the competition," said Wanderers coach Alen Stajcic.
"It's just got all the ingredients to be a successful team but you have to grow and improve, and we've done that throughout the season."
The Wanderers faithful had fallen silent when Socceroos duo Daniel Arzani and Nishan Velupillay helped put the visitors up 2-0.
Velupillay weaved past Gabe Cleur for a shot from the left side of the area, before Arzani's masterly cross to Reno Piscopo seven minutes later had the Victory well on top.
But after hitting back through Bozhidar Kraev minutes later, the Wanderers looked poised to cash in after weathering a storm just after the break.
Anthony Pantozopoulos and Alex Bonetig each came to goalkeeper Lawrence Thomas' rescue to parry away would-be Victory goals at point-blank range just after the half.
"In the end there's sliding doors moments and we didn't take those opportunities," said Victory coach Arthur Diles.
"They're a lethal team up front and they threw everything at us in that second half, and they get their reward. I still think we threw that one away."
With 15 minutes to play in regulation time, Brandon Borrello celebrated his call-up to Tony Popovic's Socceroos squad for the upcoming round of World Cup qualifiers.
The 29-year-old forward had curled a shot above the woodwork minutes earlier but made no mistake with his header after substitute Alex Gersbach crossed into the area.
It broke a 10-game scoring drought for Borrello that had stretched back to December.
Victory never again had the wealth of chances they enjoyed early in the second half as the Wanderers went into party mode late.
Melbourne defender Kasey Bos will go for scans after suffering a facial injury in a clash with Western Sydney's Zac Sapsford during the first half.
He initially played on with padding on his nose but did not take the field after half-time.
"His nose is a little bit all over the place. He wanted to keep going but from a medical point of view we had to do the right thing and put his health first," said Diles.
