Bastian Schweinsteiger and Mario Mandzukic put Bayern two goals to the good after 22 minutes before Franck Ribery and Claudio Pizarro added further strikes in the second half to extend their unbeaten run in the Bundesliga to 31.
Both sides enjoyed winning starts to their UEFA Champions League campaigns in midweek and made one change from their European outings, with Schalke bringing in Jermaine Jones in place of Marco Hoger.
Arjen Robben's corner found the unmarked midfielder, who headed into the far corner of the goal beyond the despairing lunge of defender Astuto Uchida on the line.
Mandzukic doubled Bayern's lead just a minute later, again through a header, this time from Alaba's delivery.
The Croatia international's effort beat Timo Hildebrand before striking Benedikt Howedes on the line and dribbling in.
Schalke had not conceded in three games going into Saturday's clash and will have been relieved to see Robben's strike deflected wide just short of the half-hour mark.
Mandzukic shot over from inside the area after good work from Robben on the right six minutes after the break as Pep Guardiola's side pressed for a third.
Boateng's off-target header from a Julian Draxler cross just after the hour was their first opportunity of the half but Bayern's lethal touch was soon evident again after 74 minutes.
Pizarro added a fourth seven minutes from time with a simple tap-in after good work from fellow substitute Muller to beat Hildebrand, as Bayern made it five wins from six in the league this season.
