Nils Petersen and Thomas Muller scored the goals for a Bayern side who did not even need to move out of first gear to beat the Royal Blues, who succumbed to their second straight defeat.
Bayern goalkeeper Manuel Neuer, making his first return to the Arena AufSchalke since his summer transfer between the two clubs, was nothing more than a spectator for 90 minutes, as he had been as a young boy on the terraces of Gelsenkirchen's Park Stadion.
In the day's other match, Hannover struck twice in the last five minutes to stun reigning champions Borussia Dortmund, who fell to a third defeat of the season.
Dortmund looked set for their first away win of the campaign on the back of Shinji Kagawa's well-taken 63rd-minute strike, but with four minutes to go Karim Haggui struck an equaliser and Didier Konan then kept his cool to win it in the dying seconds.
The result means Dortmund have lost three of their opening six games after waltzing to the title last season.
Werder Bremen moved to the top of the Bundesliga after a 1-1 draw at Nurnberg despite having goalkeeper Tim Wiese sent off after 16 minutes.
Heavy rain made playing conditions almost impossible and the visitors were hardly helped by the early dismissal of Wiese after he brought down defender Christian Eigler outside the penalty area.
Mehmet Ekici put Werder ahead against the run of play but Philipp Wollscheid earned his side a deserved point with his second-half goal.
Borussia Monchengladbach climbed to second after a 1-0 win at bottom side Hamburg.
Igor de Camargo headed home the game's only goal in the 66th minute to send Lucien Favre's side level on 13 points with Werder Bremen at the summit, although Bayern Munich can regain top spot tomorrow with victory at Schalke.
Hoffenheim kept up the pressure on the leaders as two goals from Roberto Firmino guided them to a 3-1 victory over Wolfsburg.
Former Liverpool forward Ryan Babel opened the scoring after 20 minutes before Brazilian Firmino doubled the lead three minutes later.
Ashkan Dejagah pulled one back before Firmino struck again four minutes from time, after Wolfsburg goalkeeper Marvin Hitz was sent off for abusive language.
Lukas Podolski inspired Cologne to a 4-1 win over Bayer Leverkusen in Stale Solbakken.
Podolski created Cologne's first goal for Milivoje Novakovic just before half-time before scoring the second just after the break.
Podolski's second and Cologne's third sealed the win in the 54th minute before Simon Rolfes grabbed a consolation for the home side.
Andre Schurrle was sent off late on before Mato Jajalo completed the scoring with Cologne's fourth deep in stoppage time.
Augsburg survived the late dismissal of Sebastien Langkamp to hold on for an decent point in a 2-2 draw at Hertha Berlin.
Hajime Hosogai fired the visitors into the lead in the first half but goals from Christian Lell and Tunay Torun early in the second period put Hertha in the driving seat.
Jan-Ingwer Callsen-Bracker's strike on 64 minutes secured a point for the promoted side, although they endured a nervy final few minutes after Langkamp saw red for a professional foul on Raffael.
Kaiserslautern came from behind to win their first Bundesliga match of the season, beating local rivals Mainz 3-1 at the Betzenberg.
Eric-Maxim Choupo-Moting gave the visitors the lead after a quarter of an hour, but an own goal from Bo Svensson brought the home side level within 10 minutes.
Itay Schechter put the Red Devils in front in the 54th minute before Christian Tiffert sealed the win in the 73rd minute.
Martin Harnik scored twice as Stuttgart closed the gap on the German Bundesliga leaders with victory at Freiburg on Friday night.
The Austria forward netted in each half to put the visitors firmly in control, Papiss Cisse's 85th-minute effort coming too late for the hosts.