The Bundesliga champions confirmed on Wednesday that the 23-year-old had suffered a fifth major knee injury in 14 months.
Thiago, who has made 15 appearances in 2014 in all competitions for Bayern, returned to full training this week and was in the frame for a place in the squad for Saturday's visit of Werder Bremen.
However, Bayern announced that he will require further surgery after suffering a partial tear of the medial collateral ligament in his right knee.
"What can I say," a disappointed Thiago told the club's official website. "Of course, I am at the moment profoundly disappointed.
"Why always me? But I will not give up, I will fight again. I'm going to get close again and I will celebrate my comeback at Bayern."
Thiago suffered his first knee injury in August 2013 during a league match with Nuremburg and, although he returned three months later, he aggravated the problem against Eintracht Braunschweig.
With the World Cup in his sights he again returned to action but suffered a third ligament tear against Hoffenheim in March, with another setback coming against Borussia Dortmund in the DFB-Pokal final in May.