Chelsea qualified for the Champions League knockout stages despite a limp performance as they were beaten by Basle for a second time in Group E.
Mohamed Salah's fine goal three minutes from time earned Basle a deserved 1-0 victory at St Jakob Park and completed a double over Jose Mourinho's Chelsea, who 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 Romanians.
The Blues, 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 Basle in the semi-finals en route to winning the Europa League.
This season, in the premier tournament, Basle 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 the Blues 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 Cameroon 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 Basle'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.
The Blues, 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.
Chelsea 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 Basle 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, the Blues 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.
Basle, 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 the ball 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.
The Blues 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 Basle 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, Basle 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.
Mourinho blames fatigue
Manager Jose Mourinho refused to blame his players for a "bad performance" as a 1-0 defeat at Basle still proved enough to send Chelsea into the Champions League knockout stages.
Mourinho blamed tiredness amongst his players for the defeat and admitted he should have made more than the one change he opted for from the side that won 3-0 at West Ham on Saturday.
Willian was the only player to come into the starting XI, at the expense of Eden Hazard, as Mohamed Salah's 87th-minute strike was the difference.
"I felt they were tired," Mourinho told Sky Sports 2.
"I think after West Ham maybe they paid the price.
"The players were tired. I'm not so sad with them. I understand.
"Maybe I should make more changes with my team. When you have that performance against West Ham you have the temptation to play the same team.
"I made one change with Eden because I felt he could come on and change the game. Maybe I should change other players."
A goalless draw between Steaua Bucharest and Schalke meant the Blues still went through, which Mourinho conceded was the only positive from the night.
"It was a bad performance," he said.
"Only because of other results we have qualified. That's the only positive thing from this night."
Asked what went wrong Mourinho, who saw his side beaten 2-1 by Basle on the opening night, added: "Everything. I didn't like it from the first minutes when immediately we made a defensive mistake.
"We should get a better result than this. I just want to prepare for the weekend.
"I don't want to blame the players."
Goalkeeper Petr Cech made a number of saves to keep the game level before Salah's late winner and admitted the Blues deserved to be beaten.
"The first half we didn't play well. The second half we improved a little," he said.
"The only positive we have is that we qualified from the group.
"Sometimes 10 points isn't enough to go through. (On this occasion) we have gone through but it is the only positive because we did not play well.
"We need to be better."