The Blues crashed to another last-gasp defeat to put them in real danger of failing to reach the Champions League knockout stage and ratchet up the pressure on Andre Villas-Boas.
For the third time on their travels in Group E, the Blues took the lead, Didier Drogba scoring only his second goal of the season shortly after half-time.
But, as against Valencia and Genk, the visitors threw away victory, substitute Eren Derdiyok equalising before Manuel Friedrich completed the comeback at the death.
To make matters worse, Valencia beat Genk 7-0 to wipe out Chelsea’s superior goal difference and leave Villas-Boas’ men needing to win or keep a clean sheet in next month’s final group game to reach the last 16.
“Our focus must be at the moment on Valencia at home,” said Villas-Boas. “We are still in front of Valencia but it will be a good head-to-head battle, decisive.
“We have to face it, put on a brave face and get back to the wins.
“We’ve been suffering a lot, conceding a lot of goals, but we haven’t conceded from a corner for a long time — I think that was the first time.
“We were compact and disciplined in set plays but one detail in the last moment (cost us).
“There are no perfect organisations. One small detail makes the whole difference and in this competition you pay heavily.
“We need to get the concentration and focus right. No excuses — if we have to go one more step up, that’s what we have to do.”
Chelsea arrived at the BayArena beset by problems and there was more bad news for the visitors when Ashley Cole cried off with an ankle injury.
Jose Bosingwa replaced him while Raul Meireles and Daniel Sturridge came into the side beaten by Liverpool on Sunday — but there was still no place for Fernando Torres.
David Luiz was retained at centre-half despite Gary Neville comparing his defending to a 10-year-old PlayStation gamer.
A boisterous home crowd almost had something to celebrate in the 32nd minute. Former Blues favourite Michael Ballack rose highest to head Gonzalo Castro’s corner back across goal and against the crossbar, with Ramires on hand to clear.
Drogba should have silenced the home fans completely six minutes before the break. Daniel Sturridge, Chelsea’s best player, played an inch-perfect through-ball and Drogba rounded Bernd Leno before lashing wildly into the side-netting.
Leverkusen were losing their discipline and Ballack became the third home player needlessly booked before half-time.
Chelsea picked up where they had left off and were in front inside three minutes of the restart. Sturridge floated another fabulous ball in to Drogba, who brilliantly held off Friedrich before turning and rifling left-footed into the bottom corner for only his second goal of the season.
And the striker almost twice laid on a second when his flick-on was headed straight at Leno by Frank Lampard and his pass set up Branislav Ivanovic for a blast also too close to the goalkeeper.
Cech made a brilliant reaction save to repel Ballack’s close-range volley. Then Kiessling should have given the Czech keeper no chance with a point-blank header soon after which he somehow sent straight at the keeper.
Sturridge almost settled the nerves with a superb 60-yard run and finish and Malouda was thwarted by a sprawling save.
Then it all went wrong. Substitute Derdiyok levelled 17 minutes from time when Sam’s cross drifted over Cech and the entire Chelsea defence, allowing Derdiyok to nod into an empty net.
And with the final whistle looming, Leverkusen’s Friedrich leapt superbly to power Castro’s corner in off the crossbar.
Afterwards Ballack sympathised with his old side.
“Every team has sometimes a difficult moment and Chelsea is in a moment like this now. I know the players are very competitive and I think they will come back.”
They’ll need to, and quickly for Villas-Boas’s sake.
BAYER LEVERKUSEN: Leno, Schwaab (Schurrle 57), Friedrich, Toprak, Kadlec (Derdiyok 71), Bender, Rolfes, Castro, Ballack, Sam, Kiessling (Oczipka 82).
CHELSEA: Cech, Ivanovic, Luiz (Alex 68), Terry, Bosingwa, Lampard, Meireles (Mikel 80), Ramires, Sturridge, Drogba, Mata (Malouda 65).
Referee: Viktor Kassai (Hungary).