But it was his poacher's goal in the 68th minute, when he took advantage of a deflected Gui Finkler shot to fire past Vedran Janjetovic, that broke a 2-2 deadlock and gave him team the ascendancy.
"Unfortunately Kosta travelling so soon after the (FFA Cup) final last week, he pulled up really sore in the first session that he had there, so he wasn't available," Muscat explained post-game.
"We flew him back this morning, had a look at him, and medically he was passed fit. But I just didn't think it was wise to risk him for any longer than that."
The victory lifts Melbourne to third spot on the competition table, one point behind ladder leaders Sydney with a game in hand.
However, Saturday's win will be the brightest feather in Muscat's cap, given it was Sydney's first loss of the season.
"We didn't come here to make a statement. We come here to perform and on the night, I thought we were exceptional," he said.
"There was a lot of talk during the week. Fortunately enough for us, we've built a culture where we leave our talking for the park." Melbourne next host Central Coast on Thursday.
-AAP