The playmaker had already missed Saturday's 5-2 victory over Eintracht Frankfurt.
"Thiago did not train today," Flick told a virtual news conference. "Unfortunately he will miss the game (at Dortmund)."
Bayern are top of the table on 61 points, four ahead of Dortmund, with seven matches remaining in the campaign.
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Victory in Dortmund would send them seven points clear and put them within touching distance of a record-extending eighth consecutive league crown.
"It is a completely different game from the first one (that Bayern won 4-0 earlier this season)," Flick said ahead of the game that will be played in an empty Dortmund stadium that normally sits 80,000 fans.
The Bundesliga restarted 10 days ago with a strict medical protocol banning fans from the stadiums to minimise the risk of infection.
"We are on a good run and have lost only twice in the last 23 games and drawn once. We relish this game. It's what this job is about and that motivates the players more," Flick added. (Reporting by Karolos Grohmann Editing by Christian Radnedge)
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