Neuer missed Bayern's last two games after sustaining a minor injury against Werder Bremen on 14 February, but had been declared fit to start the Matchday 25 curtain-raiser.
However, his comeback was cut short as the goalkeeper remained in the changing room at half-time and was replaced by Jonas Urbig.
“Manuel felt a slight twinge in his calf," head coach Vincent Kompany said after the final whistle. "The next game is coming up very soon. I don't want to speculate yet. Let's see what happens.”
