The result, earned courtesy of two second-half goals, means Bayer have to be content with the runners-up berth in Group K, where they now trail Kharkiv by three points with one match to go, the Ukrainian outfit having the better head-to-head record. Both sides had however already safely qualified for the Round of 32.
Confident start by reshuffled Bayer side
A combination of injuries and leave of absence for five first-team regulars gave Bayer's heavily-rotated starting line-up a youthful sheen to it, with four up-and-coming prospects included: full back pairing Carlinhos and Kolja Pusch, midfielder Dominik Kohr and forward Tobias Steffen, at 20, the oldest of the quartet.
That top-level inexperience notwithstanding, the Werkself made a more than solid start against a home side knocking the ball around with the confidence of a team with more than their share of South American talents on board. Indeed, Carlinhos had the first chances of note, firing narrowly wide in the 19th minute as a precursor to successive free kicks from his compatriot Renato Augusto. The playmaker's first had home keeper Oliaksandr Goryainov scrambling while the second, a minute later, flashed just wide.
Caught cold by Kharkiv
For all their dominance of possession, Kharkiv had to wait the best part of half an hour for their first opportunity of the half - a shot by Cristaldo turned round the post by Bernd Leno and in any case ruled offside. On 36 minutes, Augusto set up Junior Fernandes for an effort that hit the bar from a difficult angle, while Leno pulled off a great save from Cleiton Xavier's header shortly before half time.
A minute after the restart the contest turned the way of the home side as Fininho played a long ball into the path of Jonathan Cristaldo, who slammed past Leno for the opener. That, incidentally, was also the first goal Bayer had conceded in the entire competition. It seemed to satisfy the home side's requirements as they showed little immediate inclination to chase a follow-up, but for all their effort Bayer were making few inroads themselves up front in response.
Hosts wrap it up
Philipp Wollscheid made a couple of crucial interceptions almost back-to-back as Kharkiv threatened on the counter-attack with 20 minutes to go and in the 78th minute, head coach Sami Hyypiä threw top scorer Stefan Kießling into the fray to try and salvage a result. Instead, with five minutes remaining, it was Metalist who wrapped things up with goal number two, Marlos and Taison paving the way for Xavier to dispatch the ball past Leno with a playmaker's aplomb.
Kharkiv: Goryainov - Fininho,Torsiglieri, Gueye,Villagra - Edmar, Torres - Taison (Sharpar 88'), Willian (Marlos 72') - Cleiton Xavier - Cristaldo (Blanco 83')
Leverkusen: Leno - Carlinhos,Wollscheid, Friedrich, Pusch - Reinartz (Meffert 65')- Hegeler, Kohr - Augusto, Steffen (Ayding 46') - Fernandes (Kießling 78')
Goals: 1-0 Cristaldo (46'), 2-0 Xavier (86')