Franck Ribery put Bayern in front just before half-time and a David Alaba penalty 15 minutes from the end secured the win for the Bavarians.
They remain seven points clear at the top of the table, with Schalke now their closest challengers after a 2-1 win at home to Werder Bremen.
Aaron Hunt gave Bremen the lead after 16 minutes but Roman Neustadter equalised in the 59th minute and Julian Draxler scored the decisive goal 10 minutes later.
Defending champions Borussia Dortmund lie fourth following a 3-1 victory at bottom-placed Augsburg, whose top-flight status is looking increasingly fragile.
Marco Reus fired Dortmund in front in the eighth minute before two second-half goals from Robert Lewandowski put them in the driving seat.
Sascha Molders grabbed a consolation for Augsburg, but they remain rooted to the foot of the table with just six points from 11 games.
Hamburg managed to claim a goalless draw at Freiburg despite being reduced to 10 men for most of the match.
Hamburg were looking for a third successive away win but their hopes were hit when Paul Scharner was dismissed for a second bookable offence in the 35th minute.
The visitors seemed content to settle for a draw thereafter, although they were given a let-off in the closing stages when Jan Rosenthal's effort came back off a post.
Hoffenheim also had a man sent off but played out a 1-1 draw at Fortuna Dusseldorf.
Robbie Kruse gave Dusseldorf the lead after four minutes and Joselu equalised in the 39th minute.
The visitors then had Marvin Compper sent off in the 51st minute but held on for the point.
Saturday's Bundesliga Results
Friday's Bundesliga Result