The Germany international could be out for up to six months after sustaining the injury just 37 minutes into the action at the Allianz Arena on Saturday evening
The 23-year-old seemed to twist his knee when tussling for the ball with Mario Gotze after 37 minutes, and was immediately withdrawn from action as the Bavarians sweated over his condition.
The club have since confirmed the injury via their official Twitter account, with the Germany international potentially looking at six months on the treatment table.
The news comes as a bitter to blow to Badstuber, who only returned to action last month after suffering a ruptured thigh muscle in the defeat to Bayer Leverkusen.
He has featured 17 times for Bayern this season, but his participation for the remainder of the campaign now looks to be in major doubt.
The match finished 1-1 after the home side took the lead thanks to Toni Kroos, but six minutes later - deep into the second half - Mario Gotze equalised to earn the reigning Bundesliga champions a point.