The visitors slipped to second in their group following their draw in Belgium as Vossen and Derdiyok traded goals, allowing Chelsea to claim top spot in the section
Jelle Vossen stunned the visitors on 30 minutes as he fired home a swerving volley and the Belgians entered the half-time break with an advantage. With 11 minutes remaining, Eren Derdiyok restored parity, but the result means Chelsea finish above the German outfit.
The hosts struggled to find their rhythm early on, but avoided conceding and gained an enormous boost of confidence as Vossen redirected Ndabashinze Dugary's low cross into the back of the net.
Inspired by the opener, the hosts pressed on and two minutes later, Anthony Limbombe's brilliant cross found Fabien Camus at the back post, but the central midfielder could not hit the target.
Shortly thereafter, Jeroen Simaeys' free header forced a fine save from Bernd Leno, and near the end of the half, Vossen's strong first touch saw him waste an opportunity before he was booked for a dive.
Leverkusen were not without their share of good play and especially looked bright before the opener, with Sidney Sam providing the majority of the danger. The hosts proved to be exceptionally well-organised, however, and the only time a Bayer player managed to find his way into the penalty box with space, Eren Derdiyok was too strong with his first touch and the window of time to shoot quickly closed.
Play was rather pedestrian in the second half, perhaps with the two sides having been fully aware of the result of the other Group E match, in which Chelsea were comfortably ahead of Valencia.
Andre Schurrle was denied in a one-on-one situation by the brilliant Laszlo Koteles, and Derdiyok missed several good opportunities to get his name on the scoresheet before finally netting the equaliser from Sidney Sam's low cross.
The visitors then had a chance to grab a winner, with Sam's volley forcing another excellent save from Koteles. After Bayer switched to a three-man defence, Genk improved and nearly earned their first-ever win in the Champions League. However, Leno managed to avoid another goal, denying substitute Elyaniv Barda and Camus before the final whistle.
The result sees Leverkusen slip to second in Group E, following Chelsea's win over Valencia. The visitors qualify nonetheless, with Genk ending their European campaign in fourth.