Basel arrived in north London with a reputation for giant-killing after last year's defeat of Manchester United and Bayern Munich.
The Swiss champions lived up to the hype tonight, scoring two impressive away goals, but their task was made so much easier by some poor Spurs defending.
Valentin Stocker punished Kyle Naughton's lax marking by slotting home the first and a shell-shocked Tottenham were 2-0 down by the 34th minute when Fabian Frei was left alone to head home a corner.
Emmanuel Adebayor's fifth of the season and Gylfi Sigurdsson's second-half effort brought the scores level, but the two away goals leave Villas-Boas' men in serious danger of exiting the competition at the quarter-final stages.
Spurs went into the match in good spirits after Saturday's win against Swansea, but the Londoners were sloppy in possession at times and their reliance upon William Gallas, who had a particularly poor game, will worry their fans as they head into a tense final quarter of the season.
A stoppage-time injury to star man Bale, who had to be carried off on a stretcher with an ankle problem, will only add to those concerns.
The Europa League may be derided as the ugly sister of the Champions League but the opening 45 minutes was a real humdinger of end-to-end action, and appalling defending from the hosts.
Gallas needed treatment after being clattered by Serey Die. Spurs fans who watched the 35-year-old struggle against Inter Milan will have been wishing he stayed on the turf, but he got back up.
The Frenchman and his defensive colleagues soon came under pressure from the Swiss.
Gallas gave Marco Streller half a yard and he fired at Brad Friedel, but the American saved well. Markus Steinhofer then shot just over with a powerful volley as Spurs spent the opening exchanges on the back foot.
Villas-Boas was not helped by an injury to Aaron Lennon, who came off after 20 minutes with what appeared to be a hamstring strain.
Kyle Naughton went close with a long-range effort and Bale tested Yann Sommer twice, but the Swiss continued to rattle the Tottenham defence.
Gallas could not handle Streller's pace so he hacked the 31-year-old down and earned a booking.
Moments later Tottenham were 1-0 down. Fabian Schar went on the attack after Benoit Assou-Ekotto gifted Basel possession with a needless punt up field.
The midfielder rode two challenges and found Streller, whose shot rebounded off a post and fell to Stocker, who stroked the ball home past a stranded Friedel.
Five minutes later Basel were 2-0 up. Jan Vertonghen accidentally flicked Stocker's corner into the path of Frei, who directed his header beyond Friedel to send the travelling fans mad.
Streller out-jumped Gallas to send Stocker through on goal, but he shot just wide when he should have made it 3-0.
The miss seemed even more important when Spurs pulled one back seconds later. Adebayor swung his right leg at the ball and completely missed it, but he was given a second chance when Scott Parker's shot fell into the Togolese's path and he stabbed the ball past Sommer.
Parker then wasted a golden chance to level just before the break. With the goal gaping, Spurs' skipper for the night drilled the ball right at Lewis Holtby while the German was on the floor after he collided with Sommer.
Tottenham threw everything at the visitors in the opening stages of the second half. Sommer pulled off a world-class save to deny Naughton from long range, and when the equaliser came it was hardly a surprise.
Spurs needed a slice of luck to make it happen, though. Sigurdsson slipped inside from the right flank and fired a powerful shot that would have gone straight at Sommer had it not taken a big deflection and looped over the goalkeeper into the net.
Basel were soon back in on goal again thanks to more lax defending. This time substitute Michael Dawson mis-judged a tackle and Salah bore down on Friedel, but the Egyptian scooped the ball high and wide.
Friedel tipped Stocker's free-kick around the post and the unmarked Jacques Zoua shot wide from 10 yards as the chances continued to mount for the Swiss.
Parker put a foot in just before Stocker unleashed another shot on goal and Spurs went down to 10 men after Gallas hobbled off.
Spurs ended up playing with nine man after David Degen stood on Bale's ankle and he had to be carried off on a stretcher - a worrying sight for a clearly concerned Villas-Boas.