Manuel Friedrich headed a winning goal in added time to complete a home comeback which sealed qualification from Group E.
Friedrich was the unlikely match winner as Bayer 04 Leverkusen dramatically earned themselves a place in the round of 16 by coming from behind to end Chelsea FC's unbeaten record in Group E.
The commanding central defender headed the decisive goal in added time to send the German club to the top of the section. Didier Drogba had put Chelsea in front three minutes after the break, but Eren Derdiyok, on the pitch for barely two minutes, levelled with 17 minutes left before Friedrich's last-gasp intervention.
Robin Dutt's in-form side will look to wrap up the group by winning away to the bottom club KRC Genk on matchday six, when Chelsea will need to get the better of Valencia CF – 7-0 victors tonight – to guarantee progress along with their conquerors.
Chelsea had drawn both away matches in the section prior to arriving in Germany, but immediately looked at home in unfamiliar surroundings. Drogba dragged an early opportunity wide before Ramires released Daniel Sturridge down the right. The forward's cross was deftly handled by Bernd Leno with Drogba at close quarters.
While the visitors' passing game oozed nonchalance and no mean menace, Leverkusen produced little from their scraps of possession. Yet they came closest to opening the scoring when ex-Chelsea midfielder Michael Ballack used his prodigious spring to rise and nod Gonzalo Castro's corner off the bar with Petr Čech seemingly beaten.
Leno was equally powerless when Drogba snapped on to a Sturridge through ball. The Ivorian rounded the Leverkusen goalkeeper, but was betrayed by his balance and foiled by the ever-tightening angle as his shot drifted over the unguarded goal. Sturridge's ability to pick a pass was problematic for the hosts, and his evident understanding with Drogba was fundamental in Chelsea going ahead.
Sturridge's curling lofted ball was brilliantly brought down by his strike partner, who turned and held off Friedrich to fire low beyond Leno. It took a pair of spectacular Čech saves from Ballack to keep the English club ahead, however. An overhead kick from the 35-year-old was tipped over before, from the resulting corner, Čech threw himself at his former team-mate to brilliantly block a point-blank shot.
It was the sort of save that wins matches, but Čech's efforts ultimately counted for nothing. First Sidney Sam set up Derdiyok for the equaliser before Friedrich rose to meet Castro's corner with seconds remaining to send the BayArena into raptures and Leverkusen into the next round.