Alaba, who has been in superb form this season when fit, suffered the injury on international duty with Austria when Bosnia and Herzegovina player Ermin Bicakcic landed on his left knee.
The 22-year-old was substituted at half-time of the international friendly and Bayern have confirmed that he has suffered an medial ligament tear.
Bayern confirmed via an official statement that Alaba, who can play in defence or attack, will be in a cast for 14 days and out of action for around seven weeks in total.
With the Champions League final coming in Berlin on June 6, it seems that Alaba’s season is likely over.
Wednesday’s news is a further setback for the talented youngster, who also suffered a knee ligament injury in November in the Champions League against Roma and only returned on January 30.
“I’m obviously very said,” said Alaba. “But I have a big goal: I want to be back for the season finale.
“I will recover well now and the give it full throttle in rehab.