Berisha gave Victory the lead in the 20th minute with a sublime goal that stunned Sydney's parochial 41,546-strong crowd.
The polarising frontman took possession about 25 metres from goal and toyed with Wilkinson as he ran at the Sydney defender.
After jinking this way, then that, Berisha coolly converted during an opening half punctuated by an all-in melee.
Tempers boiled over in the 34th minute when Sydney's Milos Ninkovic was taken down by a Leigh Broxham tackle.
Ninkovic's instant remonstration escalated into a push and shove involving all players: three of them - Ninkovic, teammate Filip Holosko and Melbourne's James Troisi - were booked in the aftermath.
After trailing at halftime, Sydney were rewarded for a period of sustained pressure after substitute David Carney swung onto his right foot and fired a powerful shot.
Victory goalkeeper Lawrence Thomas got a glove on the shot and his teammate Berisha a slight nod as the ball sailed along the goal line, before Grant steamed in for a 69th minute tap-in.
With scores tied, the decider went to extra-time and Melbourne playmaker Troisi came centimetres from a winner - his crisp volley in the 107th minute struck the inside of the left-hand post.
Just three minutes later, Sky Blues stalwart Carney was brought down and tumbled into the box amid cries for a penalty, but the foul occurred centimetres outside the box.
Carney then butchered a gilt-edged chance when in time and space in the box before the penalty shootout.
- AAP
