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Melbourne Victory coach Kevin Muscat says his side thoroughly deserved all three points, after Besart Berisha netted a 90th minute winner to hand the Victory a 3-2 win in the Melbourne derby on Saturday night.

Victory led 2-0 at the 57 minute mark, before City scored two goals in three minutes to level the scores, before Berisha netted the winner.

"We got ourselves in front and then we go on and get the second. Generally when that happens everyone thinks you're going to go on and shut the game out," Muscat said.

"That's the beauty of these games, they're derbies.

"Anything can happen in these games.

"I think the positive is that we go on and find a way to score the winner.

"We almost had a winner before that (the goal) too, there was contact with Bes inside the box.

"He made sure the next time the ball came across he wasn't going to allow anyone to impede him and he got a deserved winner.

"I thought he was outstanding tonight."

Melbourne Victory next face Newcastle on Friday night at Hunter Stadium.