كتب : Amro Hassan
Bayern were already playing under immense pressure after their humiliating UEFA Champions League exit at the hands of Barcelona.
The defeat leaves Jurgen Klinsmann's men in third place with 74 points, three behind leaders Wolfsburg who will face Energie Cottbus on Sunday.
Turkish international Halil Altintop scored the only goal of the game against his brother Hamit's team on 22 minutes.
The home side had to finish the game with ten men after superstar Franck Ribery was sent-off on 76 minutes, six minutes after Schalke's Jermaine Jones was dismissed.
The defeat means that not only Bayern will be struggling to win this year's Bundesliga title, but they also have to work hard in order to secure a Champions League place.
Hamburg, who were beaten by Borussia Dortmund, and Stuttgart, who beat Eintracht Frankfurt are both level on 54 points with Bayern as the two clubs lie fifth and fourth respectively.
Watch the game's highlights