Branislav Ivanovic was caught out on the right-hand side, and the Egyptian striker advanced through on goal to strike the ball past Petr Cech.
However, despite failing to register a shot on goal throughout the 90 minutes, Chelsea qualify for the knockout stages with one match remaining after Schalke 04 could only draw 0-0 against Steaua Bucuresti.
Read below to see how the action unfolded in Switzerland.
6.49pmAfter the groups were drawn at the end of August, Chelsea were expected to ease through to the knockout stages after being handed what was perceived to be an easy group. However, they were given an early reminder at how competitive the Champions League can be when they were stunned by Basel at Stamford Bridge.
6.52pmJose Mourinho's men have recovered the situation with three successive victories to put themselves in control of Group E, and if they earn a positive result tonight, they will qualify for the last 16. However, Basel proved during the first fixture that they had the quality to trouble Chelsea, and with a passionate home crowd behind them, we could be in for a thrilling game this evening.
6.54pmThe team news is in from St Jakob-Park. Who has Mourinho opted for in his starting lineup?
7.01pmBASEL SUBSTITUTES: Vailati, P. Degen, Ajet, D. Degen, Delgado, Sauro, Sio
7.03pmSo then, what do you make of that? Chelsea have made just one change from the weekend's 3-0 win over West Ham United, with Willian replacing Eden Hazard.
7.07pmThe Blues have also welcomed back striker Fernando Torres, who returns after recovering from an injury picked up shortly before the international break. As well as Torres, Chelsea have four attacking midfielders on the bench. It surely has to be the most attacking substitutes' bench ever assembled?
7.12pmThese two teams are no strangers to each other in 2013. As well as the Champions League fixture in September, they also met during the semi-finals of the Europa League last season. The action was fiercely contested over the two legs, with two superb David Luiz efforts the difference between the teams. Luckily for Basel, the Brazilian is out with a bruised patella this evening.
7.16pmThe other match in this group this evening throws up Steaua Bucuresti hosting Schalke 04. The visitors are just a point behind Chelsea, and they also know that they can qualify for the last 16 if they win in Romania, providing that Chelsea win in Switzerland. Steaua need a victory if they are to have an chance of making the second round.
7.20pmBasel are currently in charge of the domestic scene in Switzerland. They sit top of the Super League by two points, after losing just one match in 15. They prepared for the visit of Chelsea by breezing past Thun by a 4-1 scoreline at the weekend.
7.25pmMourinho spoke yesterday about his side's hectic fixture list going into the final month of the year. He has admitted that he is keen to get their progression done and dusted with three points tonight so that he can rest players for the final group game with Bucuresti. I'd expect a strong attacking display from Chelsea tonight.
7.29pmOne selection that will likely intrigue Chelsea supporters is the inclusion of Ramires on the right-hand side. Despite being a regular in the centre of the pitch, the Brazilian has previously excelled in a right-winger role, with his most famous performance coming in the second leg at Camp Nou when Chelsea fought back against Barcelona to qualify for the Champions League final.
7.33pmPREDICTION! Basel have been known to perform well in front of their home crowd, and I expect no different tonight. However, Mourinho would have drilled into his players that he expects them to complete the job tonight, and while they could be on the back foot at times, I'm predicting an efficient 3-1 win for Chelsea.
7.40pmIf you want to keep an eye on the action in Romania between Bucuresti and Schalke, you can do so by clicking here.
7.43pmThe two teams are out on the pitch in Switzerland. We will be underway in a couple of minutes.
2 minBasel have made a fast start to this encounter, breaking twice down the left and earning a free kick in a threatening position.
3 minA superb free kick was whipped in towards the near post, and despite Streller not connecting with a glancing header, Cech does well to prevent the ball sneaking past him.
6 minThis has been all Basel so far. A rapid break down the right has the Chelsea defence in trouble, and Ivanovic is forced to clear for a corner. Nothing comes from the first set piece, but Basel have a second on the opposite side.
8 minChelsea survive after an ambitious effort flies harmlessly wide, but Mourinho's mood isn't improved when Cech dumps the goal kick straight out of play.
10 minChelsea finally get some possession in Basel's half, but they are quickly repelled and Lampard is dispossessed. St. Jakob-Park is rocking, and understandably so. It might explode should the home side score.
13 minSAVE! Frei advances towards the Chelsea defence, and for some reason, they back off. It allows the midfielder to get a shot in from 20 yards, and Cech is forced to tip the ball wide.
14 minOFF THE LINE! From the resulting corner, a Basel player gets his head on the ball, and Mikel is forced to clear off the line!
16 minThis has been an incredibly dominant start from Basel. Eto'o nearly tapped in at the other end, but moments later, Mohamed Salah forced Cech into another finger-tip save. Breathless stuff in Switzerland.
20 minThings are finally calming down at St. Jakob-Park, but Basel continue to have the majority of the ball. Mourinho will be livid with his team's start to this game, but the home side won't be able to keep this pace up for 90 minutes.
23 minSAVE! Basel are back in the ascendancy, and Cech is back in the thick of the action. The visitors failed to clear a cross from the right, and the ball fell to Salah, and while he didn't connect with his shot in the fashion that he would have liked, the Czech stopper still had to tip the ball over the crossbar.
27 minIt is still goalless in Romania between Bucuresti and Schalke. I'd be surprised if that fixture was as action-packed as this one!
31 minWe are through 30 minutes in Switzerland, and it's still much of the same. Chelsea are starting to commit more fouls too, probably through frustration, and they need half time to come sooner rather than later.
35 minWhat a challenge from Azpilicueta. Salah gets in behind the full-back, but just as he is about to shoot, the Spaniard got back to nick the ball off the Egyptian attacker.
37 minBOOKING! The first booking of the game goes to Taulant Xhaka, who mis-times a tackle on Ivanovic on the halfway line. The Albanian had very little complaints about the decision.
41 minINJURY! Samuel Eto'o overstretches for a ball when attempting a challenge, and he appears to have suffered a groin injury. The Cameroonian knew instantly that he was done for the night, and he could be missing for a significant amount of time.
42 minSUBSTITUTION! Fernando Torres has entered the action in place of Eto'o. It will be interesting to see how he copes with having to play more than a half on his own comeback from injury.
44 minMikel commits a foul on the edge of his own penalty area. It looked a soft decision, but Basel have a fantastic opportunity to test Cech just before the break.
45 minIt's an appalling attempt from Stocker, who sees the set piece hit the wall. We are into added-on time.
8.33pmJose Mourinho was on his way back to the dressing room about 40 seconds before the half-time whistle. I think that tells you everything about Chelsea's performance during the opening 45 minutes. Nevertheless, they remain level against Basel.
8.38pmThe half-time stats are pretty damning if you are a Chelsea fan. The Blues didn't have one shot on goal before the break, while Basel had nine. The Swiss side also had seven corners to Chelsea's one, also holding onto the ball for 58% of the time. Sometimes, the stats lie, but in this case, they don't.
8.43pmHowever, despite the score, despite the stats, Chelsea are heading through to the knockout stages as it stands. In the other game in the group, it's also 0-0.
48 minThere appears to be a bit more urgency about Chelsea since the restart, but passes are still being misplaced, and they aren't making any inroads on the Basel goal.
52 minI don't think either team have had the ball in the opposite penalty area during the opening seven minutes. It has been rather uneventful, but at this stage, I suppose that Chelsea will be happy with that.
54 minMourinho has his second change ready on the touchline. Eden Hazard is about to enter the action.
55 minSUBSTITUTION! Rather surprisingly, it's Oscar who makes way for the Belgian. Interesting...
57 minBasel put together their best bit of football since the interval, and manage to earn a corner. However, the delivery is poor, and Chelsea clear. Willian looks to be struggling with a knock to his knee, but I think that he will be fine to continue.
60 minWhy didn't he shoot? Hazard jinks inside a couple of players but just as he creates an opening from 20 yards out, he opts to pass to Ramires, and the ball is over-hit. You'd have fancied the Belgian to score from that distance.
63 minBOOKING! Serey Die scythes down Hazard and is rightly booked. However, the Ivorian is incensed by the decision and refuses to walk to the referee to accept his punishment, while also complaining that he didn't receive the decision himself. Less patient referees would have dismissed him for that kind of petulance.
65 minBOOKING! Mikel follows Serey Die into the book after a foul on the touchline. The Nigerian was late, but it wasn't malicious.
69 minThere's still not much happening for either team in terms of a threat on goal. Both managers must be considering alterations. There's just over 20 minutes remaining in Switzerland.
71 minSUBSTITUTION! Arlind Ajeti is entering the action in place of Xhaka. It appears to be a like-for-like replacement in defence from Murat Yakin.
74 minWhile Chelsea need to be careful not to lose this game, they also know that if they draw and Schalke win, then the Germans will be favourite to progress through as winners of the group.
77 minSUBSTITUTION! Yakin has decided to bring off top goalscorer Streller for the final 15 minutes, replacing him with Sio.
78 minIt's worth noting that Chelsea still haven't had a single attempt on goal. When was the last time that has ever happened?
80 minThey should certainly have had one then. Hazard, who has been lively since his introduction, played the ball into Lampard, but the midfielder took too much time on the ball and he was dispossessed around 12 yards from goal.
83 minEFFORT! What an effort from Serey Die! Basel pressed forward, and after a cross was only cleared to the 30-yard mark, the Ivorian struck a volley towards goal that missed the bottom corner by millimetres.
87 minDisaster for Chelsea! Ivanovic is caught out on the right-hand side, and it allows Salah through on goal. The Egyptian shows superb composure to slide the ball into the far corner, and the home crowd erupts.
89 minNow then, with the other game still goalless, Chelsea would still qualify tonight, but if Schalke nick a goal, the Blues will struggle to top the group.
9.37pmThe full-time whistle has gone in Switzerland, and Chelsea have fallen to defeat against Basel. However, it has also finished in Romania, and it's ended goalless. As a result of that, Chelsea are through!
9.38pmI'm sure that will be a small consolation to Mourinho, but he will be furious with his team's performance. They end the game without a single shot on goal.
9.40pmAll of the credit has to go to Basel though. They were rampant for the majority of the first 45 minutes, and while they didn't continue that performance after the break, they are fully deserving of securing the double over the English outfit.
9.43pmThat will be all from Sports Mole's coverage of this match, but please keep an eye out for all the reaction from Switzerland and all of the other fixtures in our comprehensive football section. Goodbye for now.