The 29-year-old Spain international lasted the entire duration of Bayern’s return to action against Union Berlin but he was unavailable for Saturday’s 5-2 victory over Eintracht Frankfurt.
Thiago could not train on Monday as Bayern stepped up preparations for Der Klassiker, with manager Hansi Flick confirming that the former Barcelona midfielder will not be available for selection at the Signal Iduna Park.
"Thiago didn't train," Flick told reporters via a virtual news conference.
"Unfortunately, he is ruled out for this game. The final secret regarding the line-up, I'd like to keep to myself."
Thiago has made 23 Bundesliga appearances this season, scoring three goals.
In Thiago’s absence, Flick will once again call upon Leon Goretzka, who was on target in the victory over Frankfurt.
"He won plenty of balls against Frankfurt and was very aggressive. That's very important for a holding midfielder," Flick added.
"He has added some muscle, which has benefited his game. Leon is developing well.
"He was a little more attacking before, as a 10 or a number eight. But, as a six, he can show off his strength, his sprints forward.
"He interprets things differently to Thiago. I'm happy to have alternatives in this position."
Bayern Munich comfortably brushed aside Dortmund 4-0 in the corresponding fixture back in November.
The Bavarians hold a four-point buffer over Lucien Favre’s men with just seven games of the season remaining.
