First half goals to Oliver Bozanic and Besart Berisha saw Victory, who dominated the first half, take home the trophy and consign Perth to back-to-back Cup final defeats.
Even a late red card to skipper Carl Valeri, while Victory were under the pump, couldn't help Glory's cause.
Perth came out firing in the second half, but the damage was already done and having Gyorgy Sandor and Chris Harold ruled out through injury didn't help matters.
Bozanic's goal was a demonstration of his composure. Nice interplay between Kosta Barbarouses and Jason Geria provided Guilherme Finkler with the ball on the byline.
His cross found Fahid Ben Khalfallah, whose shot hit the post, but Bozanic kept his head to place the ball into the top corner with a first-time finish.
In the shadow of half time, Berisha made the game safe, in front of a disappointing crowd - only a shade over 15,000 spectators.
The Victory foward kept up his record of scoring in each round of this season's FFA Cup, and to boot it was the 200th goal in the competition's short history.
Valeri sliced open the Perth defence and Berisha's finish was all class as he arrowed his shot past Ante Covic.
After a busy start by Perth, Victory came to the fore and stamped their authority on the first half.
Perth were given an almighty let off when Barbarouses's rasping volley flashed past Covic in the blink of an eye.
Unfortunately for Melbourne Victory, Mathieu Delpierre was standing in front of Covic, in an offside position, and so the strike was ruled out.
The decision was correct, but there was no doubt Covic wouldn't have saved it regardless.
Ben Khalfallah had a shot blocked by Josh Risdon, before Perth went up the other end to finally force Vukovic into some action.
Sidnei had latched on to a wonderful pass by Richard Garcia, but his near post shot was pushed away by the Perth 'keeper.
Bozanic was well placed and stayed composed to open the scoring and soon after Berisha added the second with a clinical finish.
Perth, underdogs as it were, now had a mountain to climb.
They threw caution to the wind and they began to threaten more than they had at any point in the first period.
Good work by Marc Warren teed up Diogo Ferreira, whose clean strike from distance hit the base of the far post before bouncing to safety.
Garcia went close also from distance and the feeling was that if Glory could find a goal, they were in the game.
Substitute Guyon Fernandez looked lively too, as Kenny Lowe gambled by playing two up front for the final half an hour, against a Victory side who looked incredibly weary as the half went on.
Diego Castro volleyed over after a prolonged period of head-tennis in the Victory area as Glory ramped up the pressure.
They probably deserved a goal too, but it just wasn't to be, as the match was played out to the rather unedifying sight of Dino Djulbic as a makeshift centre forward and the farcical scene of Daniel Georgievski celebrating with the crowd long after his "goal" had been ruled out for offside.
Under FFA rules, the red card for Valeri meant the Victory captain was controversially banned from the winners' on-field celebrations, a situation coach Kevin Muscat said "has to be looked at".
But Muscat was thrilled his club had become the first in Australia to win the treble.
"We put a lot of energy into getting where we were tonight and a lot of energy to take a deserved two-nil lead," he said.
"I firmly believe you get what you deserve and the boys have put in a lot of hard work and a lot of effort to get their rewards tonight.
"It's a special night."
Glory coach Kenny Lowe lauded the courage of his undermanned team.
"They are a good side, we came into their place and it is difficult," he said.
"But at least we had a go in the second half.
"I think we didn't take responsibility for the two goals and unfortunately if you give someone like Berisha an opportunity then he'll punish you."
Barbarouses was awarded the Mark Viduka Medal as best player.
Melbourne Victory 2 (Bozanic 33', Berisha 42')
Perth Glory 0
AAMI Park, Melbourne
Referee: Ben Williams
Crowd: 15,098
