The Big V cruised to a 3-0 triumph over Melbourne City on Saturday night, brushing aside their local rivals despite being without their suspended captain.
Together with former Victory boss turned national team coach Ange Postecoglou, the skipper was on hand to present the spoils of the Socceroos' successful campaign to a packed crowd at Etihad Stadium.
And the Victory faithful weren't the only ones to receive a boost from the return of the newly decorated national team player.
"Millsy's played very well in the final. He was outstanding," Muscat said.
"We made a conscious decision to make sure he came in to training on Thursday. Because I knew his presence, as soon as he walked in the door - we had a little meeting to congratulate him. And I could just sense that the players lifted with having him around. To get him in there for those two days lifted the players, without doubt.
"His character, his aura around the place as the club captain - he was successful with the national team and he comes back and hopefully he can bring us the same sort of mentality that he's had over the last month."
Despite his status and influence on the club, Muscat insisted Milligan was no certainty to displace Leigh Broxham or Carl Valeri in central midfield when Victory face Sydney FC away from home next weekend.
"We'll make that decision closer to the end of the week," he said.
"It'll be nice to have everyone available, we're almost there."
"Football's a long week. We'll recover well. Millsy's a very important player for us."
It's honours even between Victory and Sydney from two meetings so far this season, the teams having played out an entertaining 0-0 stalemate in the Harbour City before sharing the points in a 3-3 draw in December.
"We always seem to have decent games," Muscat said.
"We've drawn both of them this year. The last time we were here there was a lot of goals. Our away form has been particularly good."