Just days after beating Bundesliga rivals Schalke 5-0, goals from Mario Mandzukic, Bastian Schweinsteiger and Franck Ribery saw Bayern flexing their muscles once again in Switzerland as they improved on their 1-0 defeat at the St Jakob Park in the Champions League last season.
Bayern lead the way going into the second half of the Bundesliga season, which starts on Friday night when Schalke host Hannover.
They have a nine-point cushion over second-placed Bayer Leverkusen, who beat Nijmegen 1-0 in a warm-up match on Friday.
Elsewhere, there were wins for Hamburg, Wolfsburg, Mainz and Nurnberg, but Hannover were beaten at home by Utrecht.
Without the injured Rafael van der Vaart, Hamburg defeated Austria Vienna 2-0 thanks to goals from Heung-Min Son and Maximilian Beister while Ede was on target in Mainz's 1-0 triumph over Rot Weiss Essen.
New Nurnberg coach Michael Wiesinger saw Timo Gebhart, Timm Klose and Hanno Balitsch find the back of the net in a 3-1 win over RAEC Mons.
Finally, former Nurnberg coach Dieter Hecking saw his new club Wolfsburg tear second-division high-flyers Hertha Berlin apart 5-1.
New signing Ivan Perisic opened the scoring, with Vieirinha and Yohandry Orozco making it 3-0 before half-time.
Thomas Kahlenberg and Robin Knoche then scored in the second half as Hecking experimented without the likes of Diego, Bas Dost and Ivica Olic in his side.