Filip Holosko cancelled out James Troisi's opener for Victory but it would be super-sub Bernie Ibini who would net the winner against the ten-man hosts.
The winger scored with 25 minutes to play, out-muscling Alan Baro and Leigh Broxham as he created, and buried a one-on-one chance.
James Donachie was given his marching orders shortly after with a wretched tackle on Sydney captain Alex Brosque bringing a deserved red card, as Graham Arnold's side sealed a win that leaves them 11 points clear atop the ladder with 10 matches remaining.
A reversal of fortunes early for the Sky Blues as they were forced onto the back foot for much of the first half, with Victory piling on the pressure in the latest edition of the Big Blue.
Danny Vukovic was forced into a number early saves with Fahid Ben Khalfallah and Marco Rojas coming close.
The deadlock was broken in the 18th minute when Troisi scored with a thunderous right-footed strike, curling the ball past Vukovic from a foot outside the box after being teed-up by Rojas, as he continued his return to form with his fourth goal of the season.
Holosko levelled the score 20 minutes later, being set up by a beautiful ball from Milos Ninkovic as he headed over Lawrence Thomas and the Victory wall into the top right corner as the first half finished square.
The second was a scrappy affair as both sides struggled to break through their opponent's defence.
The match was turned on its' head however when Ibini broke free, dribbling around two defenders then powering the ball into the bottom-left corner in the 65th minute.
Melbourne almost answered from the restart as Rojas found Berisha with a low cross, but the Albanian's flick on goal was stopped by a perfectly positioned Vukovic.
The game was all but sealed in the 71st minute when Donachie took down Alex Brosque with a late sliding tackle, with the referee given no choice but to hand the defender a straight red for the reckless challenge.
