Chelsea qualified for the Champions League knockout stages despite a limp performance as Basel completed a Group E double over the Blues with a 1-0 win.
Mohamed Salah's fine goal three minutes from time earned Basel a deserved victory at St Jakob Park. Chelsea had travelled to Switzerland needing just a point to advance and a win to claim top spot in the pool. However, Schalke's 0-0 draw at Steaua Bucharest means the Blues advance to the last 16 ahead of the December 11 meeting at home to the Romanian side.
Chelsea, who have nine matches next month, last season suffered the ignominy of becoming the first winners to exit the tournament at the group stage in defence of their title, before responding by beating Basel in the semi-finals en route to winning the Europa League.
This season, in the premier tournament, Basel have exacted a semblance of revenge.
Murat Yakin's side were out to prove their win at Stamford Bridge was not a one-off as the Swiss sought a place in the knockout stages, or at least the Europa League. Mourinho promised a different Chelsea to the one which lost in the opening group game, but saw his side outplayed.
The visitors survived calls for a penalty when the ball hit Frank Lampard on the arm after 17 minutes and Petr Cech made a series of saves to keep Chelsea level, the best repelling a deflected Salah shot when the goalkeeper had already started his dive.
Fernando Torres, fit again after missing three games with an adductor injury, replaced Samuel Eto'o after 42 minutes when the striker was taken off on a stretcher after falling awkwardly and Eden Hazard followed him into the fray 10 minutes into the second half.
But neither could improve Chelsea's fortunes and Salah's strike settled matters in Basel's favour and left Mourinho and his men frustrated, beaten and with work to do.
Since losing to Basle on September 18 - a result which ended a near-10-year, 29-match unbeaten streak in the group stages - Chelsea had won 4-0 at Steaua Bucharest and twice beaten Schalke 3-0.
Chelsea, 2-1 winners at St Jakob Park in the Europa League semi-final first leg in April, were under pressure from the start on this occasion.
They might have gone in front after 15 minutes but a Branislav Ivanovic cross was just out of Eto'o's reach. Otherwise it was all Basel and Cech saved an inswinging Taulant Xhaka free-kick, reached to claw away a dangerous Valentin Stocker cross and turned a deflected Fabian Frei shot round the post. When he was beaten by Ivan Ivanov's toe-poke at a corner, John Obi Mikel scrambled clear.
Cech then tipped over Salah's drive from the edge of the area and from the resulting corner, Chelsea survived a penalty claim against Lampard when the ball ricocheted off the midfielder's arm inside the area, with referee Stephane Lannoy deeming no spot-kick.
Chelsea deployed the same three-man midfield of Mikel, Lampard and Ramires which performed so well in Saturday's 3-0 win at West Ham, with Willian's inclusion for Hazard the only change.
Basel, though, bossed central areas and the movement of Frei and Salah caused particular trouble. The pair combined and Salah struck from 12 yards, a deflection almost seeing the ball elude Cech, who was on his knees when he palmed over. Marco Streller fired wide from Salah's cross under pressure from John Terry before Cesar Azpilicueta recovered to execute a well-timed tackle on the winger as he shaped to shoot inside Chelsea's area.
Torres came on for Eto'o three minutes before the interval and, with a spark still required, Mourinho called on Hazard, who replaced Oscar after 55 minutes. Torres and Hazard combined but the latter's heavy pass to Ramires halted a promising move.
Serey Die was booked for a foul on Hazard, presenting Chelsea with a free-kick from a promising position, but Lampard's shot was poor and Ivanov cleared. It was Chelsea's only shot on target all evening.
Chelsea were more robust in the second half, but even when Yann Sommer's poor clearance presented Hazard with the ball the visitors contrived to fluff the attack.
With the game becoming more stretched as the match entered the final 10 minutes, Die fired wide at the end of a Basel counter attack and then Fabian Schar's long-range effort was held by Cech.
Kevin De Bruyne was introduced for Willian with four minutes to go but from the restart, Basel broke and scored. Salah got in behind the Chelsea defence to meet Schar's pass and drove down the right before lofting a neat finish into the net.
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