Speaking to The Herald Sun, Muscat said, "I'm going to give it a miss.
"I'm pretty good and the hamstring's coming good, but with the travel factor it just didn't make sense to try to get up and play."
Victory coach Ernie Merrick was considering using Muscat off the bench in the final but the skipper consulted with medical staff and opted for a safe approach.
"The focus has always been Round 1 against Sydney and that's what I'm aiming for.
"It is tempting to play because it is a cup and we want to win it, but this gives me a few extra days to get treatment and get maximum strength under my belt for the first game.
"I can stay at home and get three quality training sessions and treatment."