Bayern Munich midfielder Thiago Alcantara will be sidelined for several weeks after tearing an ankle ligament in Tuesday's cup victory over Roedinghausen.

The Spain international limped off 15 minutes from time following a tackle as Bayern edged past the fourth-tier side 2-1 in a second-round match played in Osnabrueck.

Thiago left the stadium on crutches, with coach Noko Kovac saying "it doesn't look good."

The diagnosis was confirmed on Wednesday, with the club saying Thiago, who had played 14 of Bayern's 15 competitive games this season, has suffered a torn ligament and a joint capsule in his right ankle.

Bayern were without defender Jerome Boateng and midfielder James Rogriguez, both ill, and injured winger Arjen Robben and defender Mats Hummels. Midfielder Corentin Tolisso and Kingsley Coman are long-term injured.

It was Bayern's second narrow win over lower-league opponents after a 1-0 victory at fourth-tier Drochtersen/Assel in the first round.

Bayern went 2-0 up early on through Sandro Wagner and a Thomas Mueller penalty. Renato Sanches then missed a penalty for Bayern before Linus Meyer scored for the hosts early in the second half.

"We've advanced, which is what we wanted," Kovac said.

"We did a good job until the second penalty. We let the ball do the work before that. We extended our lead and should have made it three, perhaps even four.

"But then the tide turned. We encouraged our opponents, we didn't play as we had planned. They pulled one back after the break and we were on tenterhooks towards the end. We made life difficult for ourselves."

Bayern midfielder Thomas Mueller said: "We've advanced, everybody knows how we did it. Every player has to think about it.

"Our performance in the first 25 minutes was good but we eased off after the missed penalty. That isn't our ambition.

"After the break and the goal we conceded we were nervous, our passes weren't accurate enough. That mustn't happen. Put it behind us and move on. But of course we must talk about it."

Bayern, who are second in the Bundesliga, two points behind Borussia Dortmund, are at home to Freiburg on Saturday before meeting AEK Athens in the Champions League. The following weekend sees them at Dortmund.