The French right-back underwent meniscus surgery in his left knee after being injured in training on Sunday and will be sidelined for several weeks, the club said.
"We have our thoughts of how to replace Sacha tomorrow and we have solutions," Bayern coach Vincent Kompany told a press conference ahead of Tuesday's game. "It is a shame for Sacha because he was in good form and I hope he is back as soon as possible.
"We have time tonight and tomorrow to discuss the situation but we have answers."
Bayern, who are top of the Bundesliga with three league wins from three matches, are starting their campaign in the hope of reaching the final to be played in their Allianz Arena in Munich in May 2025.
Tuesday's game is also the first Champions League match as a coach for former Belgium international Kompany, who took over Bayern this season.
"The dream is there for the final next year in Munich. Our fans can dream," Kompany said. "The main thing is for me that we show it on the pitch tomorrow.
"We have a tough game tomorrow and it is important to play well and win tomorrow. We hope fans can dream for a long time. We need total focus from the first to the last minute," he added.