The 30-year-old forward had been enjoying an uptick in form, re-establishing himself as one of the squad's most reliable attacking outlets.
His setback comes at a crucial moment as Bayern pursue success in two cup competitions they have not won for six years, with demanding fixtures now on the horizon.
Vice-captain Joshua Kimmich has emphasised Gnabry's importance to the team, describing him as a key and dependable figure within the squad, while also acknowledging the impact his absence will have on Bayern's immediate ambitions.
"We miss Serge terribly. In the dressing room, on the pitch," Kimmich said.
"It's a really, really big loss - both as a footballer and as a person. It's going to hurt us a lot, but I hope we can somehow compensate for it."
Despite the setback, there is some encouragement for the Bundesliga champions. Bayern have already secured the 2025/26 league title, but attention has shifted firmly towards cup success and maintaining momentum through the final stretch of the campaign.
Jamal Musiala's return to match fitness provides a timely boost to the squad, adding creativity and attacking depth.
Meanwhile, Lennart Karl and Tom Bischof are currently sidelined with injuries but are expected to return in the near future.
Bayern Munich sporting director Christoph Freund has admitted it is "tough" to discuss Joao Palhinha's long-term future at Tottenham Hotspur while the club remain locked in a relegation battle.
Manuel Neuer has hinted that his future at Bayern Munich could soon be resolved after leading his side to a long-awaited cup final with a 2-0 win over Bayer Leverkusen
Harry Kane and Luis Diaz fired Bayern Munich into the DFB-Pokal final with a 2-0 semi-final win over Bayer Leverkusen on Wednesday evening.
Fresh from sealing another league triumph, Bayern Munich turn their attention to cup ambitions as they prepare for a decisive clash against Bayer Leverkusen on Wednesday evening.
