Chelsea's campaign continues to close inexorably around them. For a while on Wednesday night the Londoners had flirted with qualification from the group phase, a rare away victory in Europe and a clean sheet to ease their recent defensive jitters. In the end, pegged back and then beaten in added time, they departed the Rhineland choked in defeat and with their confidence in tatters. Progress into the knockout phase suddenly feels in serious jeopardy.

The Germans leapfrogged Chelsea to confirm their own passage courtesy of Manuel Friedrich's header deep into stoppage time after the centre-half had leapt away from the substitute Alex to convert. Leverkusen conclude their programme with a fixture against Genk, the whipping boys, to suggest they will go on to top Group E. Chelsea require a clean sheet or a victory against Valencia in next month's finale at Stamford Bridge just to finish second. Both feel like stiff targets.

Normally, they would welcome the opportunity to have their destiny in their own hands, yet matches are veering away from them too easily. The sense that progress is inevitable – born of eight successive years in the latter stages of this competition – now feels deceptive. Indeed, the lapse of concentration in time added on was all too familiar. David Luiz may have been removed from the fray complaining of dizziness by then – the Brazilian, so gung-ho at times, had actually been more conservative in his approach here – but the fragility remained.

Alex is a rugged, aggressive defender who would have hoped to have shored up this rearguard alongside John Terry, yet he had entered with his side ahead and departed with his team-mates defeated. The Brazilian would have been dismayed that Friedrich eked out space to convert though, in truth, composure had been draining from the visitors' approach ever since their lead had been cancelled out. Theirs was a muddle in the six-yard box rather than any organised barrier. Last- minute losses no longer feel surprising.

The colour had rather drained from Villas-Boas in the aftermath, his deflated mood understandable given he has never experienced a run as dismal as this in his fledgling managerial career. His side have now lost four of their past seven games in all competitions, though the frustration here was a realisation that the Chelsea of the not-too-distant past would have prevailed having led. They had roused themselves from a becalmed opening, the shock of Michael Ballack looping a header on to the crossbar raising the visitors from their slumbers. For 20 minutes either side of the interval they dominated and squeezed out a lead in the process. Ultimately, that was still not enough to see them through.

Their passing had admittedly been sloppy even when they were in the ascendancy, Daniel Sturridge's busily slippery approach alone threatening to unsettle Bayer until the England striker found Didier Drogba three minutes after the interval. The Ivorian turned Friedrich, claimed an extra yard and rasped a left-footed shot into the corner. That was the 33-year-old's second goal of the season, and his first for two months. Drogba might have established a lead before the break, only to strike the side-netting with his shot. Even so, with Raul Meireles and Ramires offering a nervous and rejigged backline added protection, there had appeared little threat of a riposte.

Yet, even with José Bosingwa relatively impressive as a stand-in left-back for the injured Ashley Cole, the soft underbelly was to be exposed yet again. Leverkusen were becoming desperate, conscious of the cricket score Valencia were rattling up at the Mestalla, with their approach ever more direct, when Alex failed to cut out a diagonal pass from right to left which Sidney Sam collected. Petr Cech, who had expertly suffocated another Ballack attempt from close range, tore to the right of his penalty area in an attempt to snuff out the danger but Sam still mustered a cross that retreating defenders were in no position to repel. The substitute Eren Derdiyok leapt beyond the far post to convert with his first meaningful touch.

Even a draw would have represented a solid evening's work, but good fortune has long since deserted Chelsea. Lars Bender escaped after fouling Drogba in the area, the latter's team-mates left mystified and apoplectic at the decision not to award a penalty, before the cataclysm at the end.

It had once felt unthinkable that this team might fail to make the knockout phase. Now the Londoners must fret on their progress for a fortnight. These are startling times.