With the win Victory jump up to third and find themselves seven points clear of seventh place, with six rounds left for the remaining sides.
Melbourne Victory made four changes, with all four changes being forced, while the Mariners made three changes, perhaps with an eye to a midweek Champions League match.
Both sides struggled in the early going, with so many changes to the sides with neither side able to create any real chances in a tight opening.
In the 11th minute an own goal nearly gave the Mariners their opening goal with Kim Seun-Yong’s corner being redirected by Leigh Broxham in to the woodwork but Victory were spared when Duke couldn’t control the rebound.
The next chance didn’t come until the 29th minute when Guilherme Finkler hit an effort from distance that was easily saved by Liam Reddy.
Two minutes later it could well have been the Mariners who hit the lead as Mitchell Duke found Nick Fitzgerald whose header went just wide.
Those plays seemed to open the floodgates as one minute later Victory had their goal as Finkler controlled a Connor Pain pass before sending it on for James Jeggo who was able to beat his defender, and hit the ball in to the corner of the net.
That would be all the scoring in a tight and at times cagey first half, with Victory holding a 1-0 lead at the break.
The second half was much brighter with the Mariners starting well, both Fitzgerald and Duke forcing saves out of Lawrence Thomas in the early going.
Thomas was promoted to the starting goalkeeper spot after too many Nathan Coe errors, but in the 63rd minute, it became clear that Thomas was little improvement on Coe’s shambolic goalkeeping.
Thomas failed to clear and that mistake allowed Zac Anderson to sneak in and score a simple goal to make it level.
Anderson’s joy turned to despair in the 77th minute as he blocked an Archie Thompson shot with his arm, allowing James Troisi to step up and hit a powerful penalty that snuck in under the bar.
In stoppage time Victory completed the scoring as a counter attack allowed Kosta Barbarouses to sneak the ball under Liam Reddy for the vital win.