The Bavarians endured a turbulent match after falling behind early through Aleix Garcia in the sixth minute.
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The visitors also had two goals ruled out and were reduced to nine men after red cards for Nicolas Jackson in the 42nd minute and Luis Diaz, who received a second yellow in the 84th minute.
Despite the setbacks, Bayern fought back, with Diaz scoring the equaliser in the 69th minute after being set up by Michael Olise.
"That is the worst performance by a refereeing team I have ever seen in a Bundesliga match," the 74-year-old honorary president of the Munich club is quoted as saying by Bild.