كتب : Hatem Maher
Goals from Toni Kroos, Simon Rolfes and Eren Derdiyok in the first 34 minutes helped Leverkusen go to the locker room with a 3-0 lead.
Stefan Kiessling notched his sixth goal of the season midway through the second half to complete the rout.
Leverkusen have 20 points from eight games, three ahead of Hamburg who face bottom club Hertha Berlin on Sunday.
Bayern, without injured winger Arjen Robben, failed to break down Cologne's defense at Allianz Arena.
They also couldn't find the net in a 1-0 league defeat to Hamburg last week and a goalless draw with Juventus in the midweek Champions League tie.