Goals from Daniel Georgievski, Archie Thompson and a second half strike from Besart Berisha were enough to defeat the Mariners, who replied from an Eddy Bosnar free-kick.
The win meant Victory secured first place in the A-League, three points clear of nearest rival Sydney FC.
Most of the 22,285 fans remained inside AAMI Park to celebrate the triumph and the club's first trophy since 2009 and a record third premiership.
Melbourne only needed to avoid a heavy defeat against Central Coast to claim the Premiers' Plate.
Coach Kevin Muscat decided not to risk Fahid Ben Khalfallah, who would be suspended for Victory's first game of the finals if he received a yellow card.
The host had the better of the opening half but failed to create genuine goalscoring chances.
Victory finally made the breakthrough on 32 minutes. Berisha held the ball up in the box and teed it up for Georgievski on the edge of the area. The defender delightfully curled the ball into the top corner to make it 1-0.
It took barely a minute for Melbourne to double its lead. Gui Finkler swung in a corner to the near post and Thompson was perfectly placed to glance the ball into the bottom corner and give Victory a 2-0 lead.
Mariners gave themselves some hope of turning the result around in the second half when a deflected Bosnar free-kick made it 2-1 on the stroke of halftime.
Victory took just under two minutes to restore its two-goal advantage after the interval. After a swift move, Finkler scooped the ball over for Mark Milligan, who when faced with goalkeeper Matthew Nash, half-volleyed back to Berisha and the striker slotted home the host's third.
Central Coast blew a great chance to hit back at the other end. Melbourne goalkeeper Lawrence Thomas did well to deny Nick Fitzgerald in a one-on-one and Isaka Cernak blasted over with the follow up.
While Mariners had other chances to reduce the deficit and farewelled departing veterans John Hutchinson and Matt Simon, the night belonged to Victory and its passionate supporters, who began celebrating the triumph before the final whistle.
The joyous crowd chanted "Super Kevin Muscat" and there was even acknowledgement for ex-oach Ange Postecoglou.
The Socceroos boss was appointed as Victory coach three years ago to the day, and enjoyed a huge applause when showed on the big screen.
Muscat believes the Premiers' Plate was a fitting reward for the effort given by his players over the season.
"I'm over the moon, ecstatic," he said.
"You give so much, it's been a massive effort over 27 weeks.
"I'm not naive, I know there's a massive game in a couple of weeks... but to achieve this with that group, it's certainly special."
Mariners coach Tony Walmsley paid tribute to John Hutchinson, who finished his A-League career with the match.
"He's had a great send-off at home and to finish his game here with that atmosphere was fantastic," he said.
Hutchinson played in his 227th A-League match, becoming the league's most capped player, and will join Walmsley's coaching staff for next season.
