Two late Matt Simon penalties on Sunday night in injury time were the difference as Victory spoiled a 2-1 lead with two minutes to go in regular time.
The match was level 1-1 at the 78th-minute mark when Victory’s Adama Traore drove the ball into the box, but it rebounded of Kye Rowles into the net for an own-goal.
With Melbourne leading 2-1, Leigh Broxham was penalised for a hand-ball in the box in the 90th minute, with Simon slotting the levelling goal easily in extra time.
Another penalty conceded by Broxham in the box just two minutes later gave Simon a second chance to win the game, and he took it easily.
It was a tense finish to a tough match in front of a home crowd of 4957 at Central Coast Stadium.
The Mariners made nine shots on goal in the first half, the most they’ve attempted in an opening term this season.
The VAR overruled a chance for the home side to go in front early in the second half when it looked as though Rowles had scored.
The 21-year-old netted an assist from Jair in front of goal, but it was pulled back when VAR ruled he was offside.
Midway through the second half, the VAR was called on again, upholding a decision by the referee not to award the Mariners a penalty when Simon was knocked over by James Donachie in the box.
It drew the ire of home fans and Mariners star Milan Duric, who was yellow-carded in a confrontation with the referee.
Victory will face Adelaide on Friday night, while the Mariners will take on Western United in round 15.