The Spaniard was substituted off in the 3-3 Bundesliga draw against Hoffenheim at the Allianz Arena after picking up the injury, and replaced by Philipp Lahm.
Bayern confirmed on their official website that club doctor Hans-Wilhelm Mueller-Wohlfahrt suspects Thiago has suffered a partial ligament tear in his left knee.
The club will know for certain the extent of the injury when the summer signing from Barcelona undergoes an MRI scan, but they later revealed that he is set to miss 6-8 weeks, which in a worst-case scenario will effectively end his season.
"This is bad news," Pep Guardiola said. "We will miss him."
Thomas Mueller said: "This is extremely bitter and come to a catastrophic time, exactly before the important matches."
Arjen Robben added: "This is a great loss."
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