Arthur Diles' decision to swing changes after a disappointing 1-1 away draw to lowly Brisbane was vindicated as Nishan Velupillay and Bruno Fornaroli scored on their return to his starting line-up.
Zinedine Machach added a blistering strike in the 92nd minute to rub salt into the Mariners' wounds.
Victory (33 points) charged to fourth on the table with Saturday's impressive win at AAMI Park, behind Auckland FC (40), Western United (35) and Melbourne City (34).
But Mark Jackson's Mariners (21 points, goal difference of -16) are in strife, sitting 10 points behind sixth-placed Western Sydney with six games to go - starting with next Sunday's trip to Auckland.
Victory had 24 shots (nine on target) and Mitch Langerak didn't need to make a save, with the Mariners registering just one shot, and none on target.
Diles dropped Zinedine Machach, Nikos Vergos and Santos for Socceroos trio Velupillay, Fornaroli and Daniel Arzani.
New loan signing Alex Badolato, the player of the tournament in the Young Socceroos' U20 Asian Cup trumph, came off the bench for his Victory debut and impressed in his half-hour on the pitch.
Victory's opener, in the ninth minute, was all but gift-wrapped.
Mariners goalkeeper Dylan Peraic-Cullen passed up the centre for Haine Eames but the 16-year-old didn't properly control the ball and it spilled into the path of Velupillay, who made him pay with a fierce first-time strike.
Fornaroli bounced an audacious bicycle kick over the bar in the 34th minute, but seven minutes later doubled Victory's lead.
The striker timed his run to perfection, latching onto a long ball from Brendan Hamill with a wonderful first touch, before turning Brian Kaltak inside out and coolly lashing home.
Tempers threatened to boil over after the break with Mariners substitute Nicholas Duarte in the thick of everything.
Victory should have made it 3-0 in the 82nd minute but Santos couldn't quite control a wonderful ball from Badolato, while Peraic-Cullen brilliantly denied Vergos in the 90th.
But there was no stopping Machach when he received the ball 25 yards out and slammed into the top corner.
Victory next play the Wanderers away on Saturday.
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