A brace for James Troisi was the highlight of Victory's first win since January 14 but the night was not without controversy when the home side had a penalty call turned down when behind 2-1.
Bernie Ibini opened the scoring after a Joshua Rose right foot strike from the left-hand wing could only be pushed into Ibini's path by Melbourne keeper Nathan Coe.
Troisi's equaliser drew the visitors level in the closing stages of the first half before Archie Thompson gave his side the lead after 50 minutes moments before the Mariners were denied a penalty by referee Matthew Gillett when Mile Sterjovski was brought down by Pablo Contreras.
Troisi's ninth goal for the season in the 62nd minute gave the home side a two-goal buffer they never relinquished.
A dominant first-half performance laid the platform for Adelaide United to claim a 3-0 victory over Sydney FC at Allianz Stadium.
The win sees the Reds leapfrog Sydney into fifth spot on the table and leaves the Sky Blues with just four points from their last six matches.
The visitors hit a 17th-minute opener through Bruce Djite. A perfectly weighted long ball put Marcelo Carrusca into space down the right and he turned his defender before finding Djite with a clever pass. The striker was able to create separation from his defender and calmly slot the ball into the bottom right hand corner to give the visitors the lead.
Thee Reds had their second 10 minutes later when a long clearance left Fabio Ferreira one-on-one with half the field to work with. Ferriera brought the ball down neatly before outrunning the defender and firing past Janjetovic to give Adelaide a two-goal lead at the break.
Adelaide put the game to rest 10 minutes from full-time when a defensive error saw the ball fall to the visitors and a clever through ball put Sergio Cirio through on goal. Cirio unselfishly put the ball across the face of goal where it was finished at close range by Jeronimo Neumann.