Samuel Umtiti looked like he had earned a draw for Lyon when he smashed home a stunning half-volley equaliser in the 55th minute, but once again Bale came to the rescue for Spurs.
The Welshman put Tottenham ahead with another physics-defying set piece from 35 yards in first-half stoppage time, and he came up with the goods again just 10 seconds from the final whistle.
Maxime Gonalons upended Bale 20 yards out, the crowd called the 23-year-old's name, and he stepped up to crack a swirling shot over the wall and past a spinning Remy Vercoutre.
The Spurs winger, who played most of the first half up front alongside the poor Emmanuel Adebayor, has now scored seven goals in his last five games for club and country.
Andre Villas-Boas has a point when he compares his star man to Real Madrid marksman Cristiano Ronaldo.
Bale, who scored twice to beat Newcastle on Saturday, brought great relief to his manager with the winner as his team will now not require an away goal in Lyon next week to make the last 16 of a competition the Spurs boss wants to win so much.
Villas-Boas said on Wednesday that Thursday night's match represented a test of whether his team were good enough to cut it in the Champions League because of the French side's long history with European football's elite club competition.
With the raucous away following and bubbling atmosphere, it certainly felt like a Champions League fixture.
Tottenham put Lyon under pressure from the off. Benoit Assou-Ekotto played a clever one-two with Clint Dempsey in the fourth minute, but the visitors cleared when the Cameroonian whipped in a dangerous low ball.
There was no hint that Bale was set to have a successful evening in the eighth minute when he steadied himself to meet Kyle Walker's cross, but the Welshman ballooned over from 10 yards.
Villas-Boas prowled on the edge of his technical area and urged his players to take advantage of their domination.
Umtiti was being given a torrid time at left-back by Aaron Lennon, but Vercoutre remained untested in the Lyon goal.
The away side penetrated the Spurs box for the first time in the 14th minute and they should have had a penalty when Jan Vertonghen tripped Bafetimbi Gomis, but the referee waved play on, much to the anger of the Lyon bench.
Stirred by the near miss, Spurs upped the pressure on the away end. Mousa Dembele cut out three Lyon defenders with a brilliant slide-rule pass, but Adebayor thumped his first-time shot wide.
Bale trickled a weak shot in to Vercoutre's arms and the Welshman then had the worst miss of his career, shooting wide of an open goal from six yards after Walker had cut out the Lyon goalkeeper with his cross.
Villas-Boas, who had barely sat down all half, vented his anger at the makeshift gate erected by UEFA in front of the Spurs dugout.
Bale soon had his manager jumping for joy, however. Alexandre Lacazette hacked down Dembele 35 yards out and Bale lashed a dipping drive which left the beaten Vercoutre dumbfounded.
Lyon flew out of the blocks in the second half and equalised thanks to Umtiti's stunning striker.
William Gallas thought he had cleared the danger when he glanced Steed Malbranque's excellent cross clear, but the ball fell to Umtiti, who hit a peach of a half-volley straight in to the top corner past a stunned Friedel.
Lacazette almost doubled the lead six minutes later when he beat three Tottenham defenders, but veteran Friedel demonstrated the reflexes of a 20-year-old to tip the forward's shot over.
Villas-Boas introduced Lewis Holtby to add more energy to his side, but Bale remained the biggest threat to the away side.
The flying Welshman galloped past Anthony Reveillere in the dying stages, but his team-mates could not keep up with him so there was no one to tap in.
Bale continued to pile forward and found away through in injury time but Vercoutre saved well at his near post.
There was to be one last twist in the tale, however. Captain Gonalons felled Bale and he picked himself up before firing a beautiful curling shot past the French goalkeeper to send the home crowd in to ecstasy.