Ousmane Dembele and Achraf Hakimi both limped off during the match, continuing a run of fitness problems that has prevented Luis Enrique from having a full squad at any point this season.
PSG confirmed on Wednesday that Hakimi severely sprained his left ankle while Dembele suffered an injury to his left calf. Nuno Mendes, who played 90 minutes, also sprained his left knee, with all three expected to be sidelined for several weeks.
"I can't remember a single match with the whole squad fit. It's a different kind of season, and we have to manage that. I'm calm and confident we'll recover our players and our level," the Spaniard said.
The latest setbacks came just as the squad was beginning to stabilise.
Hakimi on crutches
Dembele, who missed seven games earlier this season with a hamstring injury, was making his first Champions League start of the campaign but was forced off after 25 minutes with what appeared to be a calf problem.
"The injury has nothing to do with the previous one," Luis Enrique told reporters. "He played the time you saw - it's not a relapse."
Shortly before half-time, Hakimi also had to leave the field after a dangerous tackle from Bayern's Luis Diaz, who was sent off for the challenge.
The Moroccan full back, one of the few PSG regulars to have avoided injury this season, left the pitch in tears and was later seen exiting the Parc des Princes on crutches with a protective boot on his left foot.
Contact sport
"For Hakimi, that's football - it's a contact sport," Luis Enrique said. "It's unfortunate, but these are actions that happen with a bit of bad luck."
The injuries add to a long list of absentees that has already included Marquinhos, Joao Neves, Bradley Barcola, Desire Doue and Fabian Ruiz - all sidelined at various points since August.
Doue is currently out with a right thigh muscle injury that will keep him unavailable for several more weeks.
After an exceptional 2024-25 season that stretched across 65 matches and yielded four trophies - the Champions League, Ligue 1, French Cup and Trophee des Champions - PSG now appear to be paying the physical price.
Their extended campaign ended only in mid-July after the Club World Cup, leaving little time for rest before the new season began.
Long season for PSG
"When you recover injured players, they're not at 100%. That's something I need to manage better," Luis Enrique conceded. "It's a long season, and it's about how you handle these moments."
Despite the disruptions, PSG remain top of Ligue 1 and third in the Champions League's league phase with nine points from four games.
Luis Enrique's tone remained measured as he looked ahead. "I'm calm and relaxed because I know we'll overcome all of this," he said. "We'll get our players back and we'll find our level again."
Check out the match report from Tuesday's loss with Flashscore.