Germany international Neuer was replaced at halftime by 20-year-old reserve team keeper Lukas Raeder, who conceded two goals in the opening 12 minutes of his Bundesliga debut, with second choice Tom Starke also out injured.
"It is not at risk," Neuer told reporters when asked whether his participation in Wednesday's game was in doubt.
"I was not taken off for no reason. We did not want to risk anything because for us it was more important for me to be fit on Wednesday," said Neuer.
Bayern, looking for an unprecedented back-to-back treble, are also through to the Champions League last four in which they will face Real Madrid later this month.
- Sports & Recreation