Bayern went with a single change from the come from behind win over Vfl Wolfsburg, as Alphonso Davies started ahead of Leroy Sane in an advancing role.
Leverkusen put their noses in front in the 14 minute when an unmarked Patrick Schick drilled a sumptuous volley from a short corner by Leon Bailey beyond Manuel Neuer.
The Bavarian squandered a big chance to draw level after a cutback into the area from Davies trickled to Robert Lewandowski, who uncharacteristically dragged off target.
Schick put the home side two goals up before the half-hour mark when he charged into the box for a bottom-low finish, but it was called for offside with the Video Assistant Referee (VAR) in unison.
An enforced substitution from the Bavarians in the closing minutes to halftime had Kingsley Coman making way for Sane.
Bayern levelled it up on 43 minutes when Lewandowski made the most of a defensive mix-up between Lukas Hradecky and Edmond Tapsoba to fire into an empty net.
Lewandowski could've finished the half with a brace after meeting a near post free-kick by Sane, but the Polish man headed over the top.
Bayern started the second with the same energy, as a half-chance in the area went the way of Serge Gnabry after good work from Thomas Muller but Hradecky parried. .
Leverkusen lived dangerously in the last 12 minutes when a loose ball on the edge of the area found Jamal Musiala, who cracked the face of the post following a low effort.
The Bavarians snatched all the points at the death after Lewandowski's close-range shot deflected off Tapsoba and into the net following a pass from Joshua Kimmich, as it ended 2-1.