The Spain international has partially torn a ligament in his right knee - the one he initially tore in March, the club announced on Wednesday.
Thiago was out of action for two months but aggravated the injury in May during training and required surgery.
It kept him out of the World Cup, but the 23-year-old had been expected to return to action in the coming weeks.
"What can I say?" said the midfielder in a statement.

"Obviously I am deeply disappointed and frustrated. Why always me? But I will not give up. I will continue to fight,” he added.
The player, who joined Bayern last season, is expected to be out of action for several more months.

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