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Erik Paartalu's injury-time header inflicted a first defeat of the A-League season on the Big V, who have three more games before the competition goes on hiatus for the AFC Asian Cup.
While at least one member of the Victory squad, Socceroo Mark Milligan, will be on international duty, the other players shouldn't expect their workload to ease off.
"We're not going to go away, we're going to train and we're going to work hard," Muscat said with a gleam in his eye when asked if the break would be welcomed by Victory.
"We'll have some time off but not too much. We'll work through, we'll work hard. We've got a lot to work on so we'll use that time."
The Victory coach paid tribute to his team's conquerors at AAMI Park, City having fully merited their dramatic win.
"They played well tonight. I thought it was a good game of football. It was a game no-one wanted to lose. The loss was always going to come. (It's) disappointing for our fans and members.
"It was always going to end up where teams become hard to beat, everyone gets a good look at each," he added, referring to the even nature of the league so far this season.
Having seen Milligan banned for three matches following his elbow on Sydney FC's Terry Antonis, Muscat was aggrieved City's Jacob Melling escaped with just a yellow card for swinging his arm in Leigh Broxham's direction.
"Well I've just seen the referee's report. And it states he's booked him for a reckless elbow. They're not my words. That's what's on the report."
A disallowed goal from Fahid Ben Khalfallah also came under scrutiny in the post-match press conference, Muscat bemoaning his team's misfortune in recent weeks.
"I don't know who the offside's been given against," he said.
"If it's against Bes in the box, I've seen he's not offside.
"If it's against Fahid, when Bes makes contact with the ball, Fahid is outside the six-yard box. So he can't be offside either. Again, it's a decision that's gone against us. Things aren't going for us, we've got to be better."