The 22-year-old Spain international was replaced by Thomas Müller in the 62nd minute of the Bavarian derby after taking a knock to his right ankle.
Six weeks on crutches
Tests on Sunday revealed the extent of the ligament damage and the Spain Under-21 European Champion underwent surgery on Monday morning with the operation branded a success.
Nevertheless, the 22-year-old will now spend the next five to six weeks on crutches before starting light training once again. He will then need a few more weeks before being fully fit, which suggests a return in November.
"We're going to miss him, he'll be out for a long time," said Bayern coach Pep Guardiola about the player he wanted more than anybody when he became coach of the record German champions. "He's a special player and very important."
Thiago will miss Tuesday night's clash with SC Freiburg, the UEFA Super Cup final with Chelsea on Friday and a whole host of games over the coming two months, including the start of theUEFA Champions League holders' defence of their title.