His through-ball found Berisha for a powerful finish into the top left corner, only for the video assistant referee to rule offside and disallow the goal.
Melbourne's inability to finish chances was cruelly punished after 29 minutes.
Scott Galloway sent in the perfect cross and Kaludjerovic's powerful header left Victory goalkeeper Lawrence Thomas no chance.
Barely two minutes later, the 30-year-old Serbian striker doubled the scoreline, this time nodding home from Tom Doyle's well-weighted cross.
Melbourne's fortunes did not look to be improving from the restart.
It took barely three minutes for the visitors to fashion their first chance, Leroy George bursting through to confront Nix keeper Lewis Italiano one-on-one before spraying his shot wide
But after 54 minutes the visitors hauled a goal back, set up after a strong strike from Barbarouses was parried and fell kindly for Berisha to tap home.
The equaliser came three minutes later from a corner, an own-goal ricocheting in off Paracki.
There were still plenty more chances for Melbourne to squander, Berisha's radar well off in firing high after Troisi's superb work along the baseline left him with a sitter.
But Berisha redeemed himself with an 86th minute through-ball for Troisi to guide home for the winner.
-NZN
