The Germany international midfielder, who initially went under the knife in June, missed almost three weeks of action after being withdrawn with an ankle problem during the 1-1 draw with Freiburg in August.
And although he subsequently returned to full training to take his Bundesliga appearances to 10 matches for the reigning champions so far this term, the 29-year-old admits that he has still been struggling with the complaint.
"The last few weeks for me were always very painful," Schweinsteiger said in a statement on Bayern's official website.
"I tried it again, but I am now at a point where surgical intervention can no longer be avoided.
"I hope that I can be completely free of pain after the surgery play football again."
Bayern have not yet put a timescale on Schweinsteiger's return, but his absence is likely to be keenly felt by coach Pep Guardiola.
