The game ended 1-1 after extra time.
In the shootout, Brosque opened the scoring, Troisi replied to kick off the shooout.
Wilkinson then missed to give Victory the advantage, and Broxham made it 2-1.
Carney coolly made it 2-2 and Valeri smashed his shot against the bar to hand Sydney a lifeline.
O’Neill scored to make it 3-2 with Rojas to take for the Big V. Vukovic saved brilliantly.
And the player of the season Milos Ninkovic stepped up to score the winner 4-2.
After confirming the Premiership with weeks left in the regular season, Graham Arnold's Sky Blues have now done the double to cement their position as the A-League's most dominant club side - and one of the greatest in league history.
Sunday's finale in the Harbour City wasn't one of the great grand finals but it was certainly the most intense.
It was a frantic and electrically charged first half as both sides threw themselves into the contest in front of 41,546 fans.
It was fierce, feisty and intense football with referee Jarred Gillett having his hands full.
Amid the scrappy play, one moment of pure class broke the game open when Berisha pounced to give Victory the lead on 20 minutes.
Sydney FC, as expected threw everything at their opponent in the second half with David Carney thrown on early, but Victory kept their shape and excellent defensive discipline.
That was till the Sky Blues’ pressure finally paid off and Rhyan Grant as popped up in the box to tap in the equaliser.
Suddenly, and for the first time, Victory were looking shaky as the Sky Blues sensed it was their time.
But in a game of few clear chances, neither side could find a winner and the game went to extra time.
Clearly both sides looked fatigued in the final stages of the finale after an epic 90 minutes.
Troisi could’ve won it for the Big V but it wasn’t to be and so to penalties it went.
1-0 Besart Berisha, Victory 20’
Rojas was crunched by two Sky Blues near the centre circle, Valeri picked up the loose ball, fed Berisha centrally, and the Big V talisman drove into the box, shifted the ball onto his left foot and powered home a low shot into the corner of the net.
1-1 Rhyan Grant, Sydney FC 69’
Sydney FC finally found enough space to get a shot off, with Carney’s effort parried onto the post and as the ball rolled along the line Rhyan Grant was first to it to drill home.
James Troisi, in the first minute of the second half in extra time, turned and shot brilliantly to beat Vukovic but not the post. A goal then and Victory may’ve been able to hold on for a win in extra time.
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