The Brazil international was sent off in injury time of Saturday's Der Klassiker after lashing out at Dortmund's Henrikh Mkhitaryan.
By then the game as a contest was already over, as Jurgen Klopp's tactical masterclass earned a 3-0 triumph for Dortmund against the Bundesliga champions at the Allianz Arena.
The German Football Association (DFB) took a dim view of Rafinha's actions, however, and subsequently handed out a three-match suspension.
Subsequently, Rafinha will miss the league matches with Eintracht Braunschweig, Werder Bremen and Hamburg, but will return for the final game of the season at home to Stuttgart.
"After his red card (against Borussia Dortmund), Rafinha has been handed a three-match ban suspension for violent conduct," Bayern posted on their official Twitter account.
Meanwhile, goalkeeper Manuel Neuer has trained alone in a bid to be fit for Bayern's DFB-Pokal semi-final with Kaiserslautern on Wednesday.
The Germany international was withdrawn at half-time against Dortmund with a suspected calf injury, and it remains to be seen whether he will be fit to face Kosta Runjaic's men.
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