A-League Wrap: Victory return to winning ways
James Troisi scored twice as the visitors recovered from Bernie Ibini's opener, with Archie Thompson also on target for the Victory.
The Mariners were left to rue a controversial decision from referee Matthew Gillett, who only awarded a free-kick when Mile Sterjovski was brought down by Pablo Contreras apparently inside the area when the home side trailed 2-1.
Ibini put the Mariners ahead with 11 minutes on the clock, turning home from close range after Nathan Coe had parried Joshua Rose's strike.
Troisi levelled on the stroke of half-time from inside the box, and the second half belonged to Melbourne.
Adam Traore set up Thompson to hand the visitors the lead five minutes after the interval and the penalty controversy followed two minutes later.
Still frustrated by that questionable call, Central Coast fell further behind in the 62nd minute as Troisi beat Liam Reddy at his near post.
Both sides have 27 points, with Central Coast in third by virtue of goal difference.
Elsewhere on Saturday, Adelaide United were comfortable 3-0 winners over Sydney.
First-half goals from Bruce Djite and Fabio Ferreira put United in control, with Jeronimo Neumann's late strike rounding off the scoring.