Bayern begin their title defence at the Allianz Arena, but Musiala will not be involved as the club continues to take a cautious approach with the Germany international.
"Basically, Jamal's doing pretty well. He'll take part in team training today. He won't be in the squad tomorrow," Kompany said.
The Bayern coach added that Musiala is still adapting to an increased dosage of medication and that his return will be decided in consultation with medical experts.
"He will return to the squad at some point and we'll make the decision in close consultation with the experts. He's doing well," Kompany said.
There was better news for Bayern elsewhere in the squad, with 18-year-old Lennart Karl returning after recovering from the injury that ruled him out shortly before Germany's 2026 FIFA World Cup campaign.
New signing Ismael Saibari is also close to full fitness, although Kompany will wait until after training before deciding whether he can start against Stuttgart.
"Lennart Karl is back in the squad; we'll have to wait and see just how big a role he can play," Kompany said.
"Ismael Saibari is making very good progress; we'll see whether he's ready to start. We've got so many matches coming up in the next few weeks."
Nathaniel Brown is another option for Kompany after impressing in an attacking role during Bayern's 2-1 DFL-Supercup victory over Borussia Dortmund. The natural left-back scored in that game and could again be used further forward.
Kompany explained that Bayern's system allows versatile players to operate in different positions.
"You've watched the games where Raphael Guerreiro has also played in the number 10 role at times. The number 10 position and the full-back position have a lot in common for us when it comes to attacking," he said.
Brown has also played in midfield during his youth career, giving Kompany another flexible option.
"He's slated to play as a full-back, but he can play in a whole host of other positions," Kompany said. "We've got a strong squad; sometimes it's better to have a few players who can play in multiple positions than to have more players in the squad."
