Spain international Thiago has been plagued by a long-standing complaint since first suffering an injury in August last year, and his recovery has repeatedly hit setbacks over the past 14 months.
The latest of those came in training this week, and it was announced the 23-year-old had sustained a partial tear of the medial collateral ligament in his right knee.
Thiago had been treated with cortisone injections when the problem first surfaced, and Guardiola admitted that may have been to his detriment.
"Maybe it was a big mistake," he said in a press conference on Friday.
"I'm sad for him. He's of course upset and disappointed. He needs a little time for himself and his family.
"No words can help him. He will look and move forward. I'm sure it will be fine again. We, the club are there for him."
Germn champions Bayern will protect their unbeaten start to the 2014-15 Bundesliga campaign when they host Werder Bremen on Saturday.
