The Bavarians revealed the Spain international has suffered a ligament tear in his knee on Saturday, with his World Cup participation now in doubt
The Spain international was forced off just 25 minutes into Saturday's Bundesliga clash with Hoffenheim and the Bavarians have now confirmed that the ex-Barcelona starlet will be out until at least mid-May and possibly until June.
"The first suspicions have unfortunately been confirmed," a statement on Bayern's website read. "Thiago picked up a tough injury in the 3-3 draw against Hoffenheim.
"After an MRI scan the diagnosis is now clear: Thiago has an extensive partial tear of the medial collateral ligament in his right knee knee.
"The Spaniard will be in a cast for 14 days. Overall, the summer signing will miss six-to-eight weeks. Thiago will definitely miss the two quarter-finals of the Champions League against Manchester United as well as possible semi-finals."
Thiago could make a return in time to feature in the Champions League final, should the European champions reach their third consecutive showpiece event, but it is unlikely he will be fit enough to be thrown into the starting XI even if he is.
Saturday was a disappointing day for Bayern as they also saw their 19-game winning streak in the Bundesliga come to an end, with Hoffenheim earning a 3-3 draw at the Allianz Arena.
However, coach Pep Guardiola rested a number of key players ahead of Tuesday's last-eight first-leg clash with Man Utd at Old Trafford.