The Germany international was sent off in the 17th minute of the Bundesliga meeting at the Allianz Arena for bringing down Schalke forward Sidney Sam.
Eric Maxim Choupo-Moting saw his resulting tame penalty saved by Manuel Neuer. Bayern then took the lead through an Arjen Robben header in the 67th minute, only for Benedikt Howedes to equalise five minutes later.
That result followed a 4-1 loss at Wolfsburg, and Bayern will now aim to get back to winning ways without Boateng, who will miss Saturday's trip to Stuttgart as well as the league games with Hamburg and Paderborn.
A statement on the German Football Association's (DFB) official website read: "The DFB Disciplinary Board have been advised by the DFB's Supervisory Committee to hand FC Bayern Munich's Jerome Boateng a ban of three Bundesliga games for unsportsmanlike conduct.
"Boateng was sent off in the 17th minute by referee Bastian Dankert [Rostock] of Bayern's Bundesliga game against FC Schalke 04 on 3rd February 2015.
"The club has 24 hours to request a hearing before the DFB disciplinary board."
