Murat Yakin's impressive visitors took a 2-0 first-half lead through Valentin Stocker and Fabian Frei before Emmanuel Adebayor and Gylfi Sigurdsson struck to rescue a draw
The Welshman was stretchered off in the final minutes after Valentin Stocker and Fabian Frei had sent the Swiss side into a shock first-half lead before Emmanuel Adebayor initiated the comeback by striking shortly before the break.
Gylfi Sigurdsson's deflected effort brought the home team level but Basel will welcome its English counterparts to St Jakob Park with the tie level and two away goals to their name.
Spurs were missing Jermain Defoe due to a muscle injury so Adebayor started in attack alongside Bale. Brad Friedel, meanwhile, got the nod in goal after Hugo Lloris picked up a knee injury on international duty, although the Frenchman was on the bench.
Marco Streller led the line for Basel, with Mohamed Salah and Stocker offering support from either wing. Murat Yakin's team, then under the management of Heiko Vogel, will be most known to English fans for knocking Manchester United out of the Champions League last season.
They have since lost impressive youngster Xherdan Shaqiri to Bayern Munich but knocked out Zenit St Petersburg in the last round of the competition. Spurs, if they were not already, were quickly made aware of the threat posed by their opponents when Streller tested Friedel before Markus Steinhofer volleyed over the bar.
Bale and Kyle Naughton went close as Spurs belatedly woke from their slumber but Basel's significant threat on the break remained and Andre Villas-Boas' side could have few complaints when Stocker converted into an open goal after Streller had turned to receive Salah's cross and hit the post.
Soon after, the hosts were left to pick up the pieces of their promising Europa League campaign when Frei headed home at the back post following Jan Vertonghen's inadvertent flick-on from a corner.
Friedel may be disappointed not to have saved the midfielder's header and Stocker took advantage of more shambolic Tottenham defending when he ran past Vertonghen and Naughton only to chip narrowly wide of goal.
Despite losing Aaron Lennon to injury, Spurs finally mustered a response as the half drew to a close. Bale's cross from the right squirmed through to Scott Parker at the back post and his volley back across goal was smashed into the roof of the net by Adebayor.
Parker should have leveled the tie when Lewis Holtby was denied following a brilliant through ball by substitute Sigurdsson but the former Chelsea man inexplicably shot wide with the goal at his mercy.
Naughton, though defensively suspect at times, was proving a active in attack and forced Sommer into a flying save with a volley 10 minutes after the break. The goalkeeper could do nothing, though, when Sigurdsson stepped inside from the left flank and took aim from 25 yards only to see his attempt deflect off Fabian Schar and loop into the top corner.
Benoit Assou-Ekotto was withdrawn for Michael Dawson, with Vertonghen moving to left back, but that did not immediately quiet the excellent Salah on the Basel right. The Egyptian sped through on goal immediately after Sigurdsson's leveller but could not keep his left-footed shot down.
And Basel, undeterred by the Spurs comeback, finished the game in the ascendancy. Salah and Steinhofer continued to combine to great effect and substitute Jacques Zoua should have converted the latter's cut-back. On this evidence, a real challenge awaits Spurs in Switzerland, and they may face it without Bale after their star was hauled off in some pain.