The 22-year-old played his first full 90 minutes since returning from injury in the 2-0 win over Eintracht Braunschweig on Saturday.
Thiago has struggled to feature for the German champions after sustaining a knee injury, though Guardiola was full of praise for the former Barcelona man's bravery in pushing his way back to full fitness.
"We have a lot of injured players and Thiago wasn't fit enough to play a full 90-minute game before," Guardiola told reporters. "He is a courageous player but still needs time to get back to full fitness.
"I'm happy about his performance, he is a player that doesn't know the word fear. He is very brave - I am satisfied, to come back like this after a three-month absence.
"That shows very strong character and it's a great effort from him, I'm happy with his performance."
Thiago joined Bayern from Barcelona in the summer transfer window.