Tottenham appeared to be heading out after Maxime Gonalons' goal, but a brilliant late effort from Moussa Dembele gave them the result they needed.
With Lyon needing a goal, Tottenham appeared to get off to the comfortable start their position deserved, passing the ball crisply and looking assured in possession. Unsurprisingly, a Gareth Bale set-piece gave them an early chance, but it was a cross rather than a direct effort, and William Gallas proved unable to guide his header on-target.
Yet early on, disaster struck for the visitors. Another set-piece goal went to Lyon, as Kyle Walker showed some typically reckless defending to give them a free-kick in a dangerous position, from which Maxime Gonalons headed his side ahead at the far post.
That left Spurs the side needing to score, and under the pressure, the fluency quickly seemed to evaporate from their performance. The rest of the half saw few chances, with Bale looking out of sorts - even when having a poor game, the Welshman still looks dangerous, but his runs ended too often with the ball overhit, and Tottenham's midfield were struggling to pass their way through the massed Lyon ranks.
With their creativity and vision failing them, Lewis Holtby did resort to one long-range effort in particular which came close to putting them back in the lead, but his effort from outside the area was pushed into the post by Remy Vercoutre, and the half ended 1-0 to the hosts.
Emmanuel Adebayor had been Tottenham's best player, although had not been adequately supplied by the likes of Bale - just as the second half began, their roles reversed, the Togolese striker sending in a fine cross for Bale to inexplicably sidefoot wide from just ten yards. It was hardly a sitter, but it was still a poor finish from the winger, and indicative of his night overall.
Spurs had the better chances, but it was hardly attack versus defence, and Lyon almost got their second goal during one nervy spell for Spurs midway through the second half - Clement Grenier first went close, getting on the end of a cross for a finish which Brad Friedel was fortunate to keep out with his legs, before the veteran keeper then appeared to bring down Alexandre Lacazette as the Spurs defence went AWOL, although the replay showed that there was little if any contact made.
The passage of time led Lyon to retreat ever-deeper, however, and a Tottenham side that was already struggling for fluidity and creativity was reduced to resorting to even more long shots - Bale was, of course, their principal threat, but could not find a way past Vercoutre.
As injury time dawned, however, and Spurs perhaps looking at their least likely to score, they got the breakthrough from one of their players who had until then put in perhaps the most mediocre performance of the night. Lyon's policy of standing off rather than pressing gave Moussa Dembele enough freedom outside the area to leave Gonalons in a heap before hammering a left-footed shot from the edge of the box that finally beat Vercoutre and gave Tottenham progress to the second round.
Andre Villas-Boas will be pleased that his side showed enough determination to secure the result they needed, but even with Holtby, there are still huge concerns over Spurs' ability to make the most of their dominance in games. More creativity must come from somewhere - they certainly have the players, but at the moment they look reliant on individual moments of brilliance.
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