A solitary switch from the win over Vfl Wolfsburg set out Bayern's changes as Leroy Sane missed out and Kingsley Coman earned a recall on the wings.
Bayern laid their intentions bare inside seven minutes after Eric Maxim Choupo-Moting charged in the middle of the area to volley home a rebound from goalkeeper Lukas Hradecky.
The Bavarians made it two goals six minutes later when Joshua Kimmich feed on a loose clearance from Daley Sinkgraven on the edge of the area to apply a first-time finish past Hradecky.
Uncomfortable bit of goalkeeping from the latter six minutes to halftime led Choupo-Moting closer to a brace from a loose pass off Joshua Kimmich's effort, but in the end he went wide.
Leverkusen issued a double change following the start of the second half in Florian Wirtz for Jeremie Frimpong and Karim Bellarabi included ahead of Moussa Diaby.
Choupo-Moting added a second to his tally following the midway stage of the second half after following up a ball over the top from Kimmich, but he was flagged for offside.
Within moments the Bavarians provided another smart opening from a loose ball on the area following a corner-kick, but it was drilled over by substitute Sane.
Leverkusen had the Bavarians on a knife edge following the last 20 minutes after Bellarabi send a ball from Leon Bailey off the ground and onto the crossbar.
Further duties followed the treble champions inside fulltime with goalkeeper Manuel Neuer produced into a succession of saves from Nadiem Amiri and Bellarabi.
The Bavarians still had chances to add more goals, but Jamal Musiala in particular couldn't profit however the match finished 2-0 and such see Bayern go ten points clear at the top of the table.