Fourth on goal difference, a double to James Troisi was the highlight of the side's first win since January 14 (when they beat the Western Sydney Wanderers) 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.
Early on Zac Anderson had an attempt cleared off the line inside three minutes by Victory defender Scott Galloway after the defender headed a Sterjovski corner towards goal.
Central Coast continued to press and got their reward when Ibini found the back of the net after Coe failed to deal with Rose's shot.
Victory midfielder Gui Finkler, who was prominent in the first half, should have done better in the 37th minute after a ball was played in to him at close-range. Finkler's shot was deflected away by Storm Roux.
Melbourne were getting some chances in transition, primarily through the middle of the park, but it wasn't until the dead-ball scenario in injury time which created a goal.
Finkler's free kick was flicked away by Liam Reddy onto his post and into the path of Troisi, who took advantage of the sleeping Mariners defence.
The goal gave Kevin Mucast's men some much-needed reward before the interval and after Adam Traore beat Roux to set up Thompson the visitors had a surprising lead.
Two minutes later referee Gillett turned down the home side's penalty appeals to award a free kick outside the area. The resulting free kick was another left-foot blast from debutant Eddy Bosnar, this time saved by Coe near the top right hand corner.
After Sterjovki fired wide in the 58th minute Troisi's double was set-up when Tom Rogic flicked a neat pass to the 25 year-old who beat Reddy at his near post.
The Mariners cleared their bench late, including brining on Cernak and striker Mitchell Duke but were unable to create enough to trouble Melbourne.
Deep into injury time Melbourne substitute Adrian Leijer went off after coping a stray boot to the head which will be monitored.
Melbourne Victory 3 (Troisi 45+, 62, Thompson 50)
Central Coast Mariners 1 (Ibini 11)
Crowd: 9,138 @ Bluetongue Stadium
