Lyon bowed out of the Champions League after they were beaten 2-1 by Gent in France on Tuesday.
The home side - playing their final European game at the Stade de Gerland before leaving for the Stade des Lumieres - opened the scoring through Jordan Ferri's close-range finish but a fine free-kick from Danijel Milicevic levelled the game before half-time.
Gent goalkeeper Matz Sels was fortunate not to be sent off for a handball and proceeded to frustrate Lyon for much of the second period, making a string of brilliant saves to keep the scores level.
Lyon dominated the majority of the closing stages but were unable to find the goal that would keep alive their hopes of reaching the knockout stage before their matchday six showdown with Valencia.
And Gent found a crucial winner in the dying seconds of injury time through substitute Kalifa Coulibaly, meaning they leapfrog Nuno Espirito Santo's side into second place ahead of their meeting with runaway group leaders Zenit, while Lyon crash out of Europe altogether.
With just one point from their opening four matches, Lyon were in desperate need of a strong start and they managed just that - albeit in controversial circumstances.
A loose ball broke to Rachid Gezzal on the edge of the area and he slipped it through to Ferri, who calmly side-footed past Sels and into the near bottom corner, though replays indicated he was fractionally offside.
Lyon goalkeeper Anthony Lopes tipped a glancing header by Renato Neto over the crossbar before Sels survived his own moment of controversy, handling Alexandre Lacazette's header outside of the box as the striker was played clean through, though the officials failed to spot it.
Sels denied Lacazette at full stretch moments later before Brecht Dejaegere blazed over from close range at the other end as the match remained wide open, and Gent deservedly drew level in some style on 32 minutes as Milicevic bent a superb free-kick beyond Lopes from 20 yards.
Mathieu Valbuena began to exert an influence over the game and slipped in Rafael da Silva to sting the palms of Sels before fizzing an effort of his own just wide shortly before the break.
Another smart Sels stop denied Valbuena's far-post volley early in the second half and he stood up superbly to parry Ghezzal's drive from the left of the box as Lyon pushed hard for the lead.
Gent began to withdraw into their half in order to preserve the 1-1 scoreline and Lyon threw on Claudio Beauvue and Maxwell Cornet as they sought that crucial second goal.
But they were undone as Coulibaly - introduced in stoppage time to run the clock down - bundled Milicevic's corner home to put the Belgians in charge of their own fate and eliminate Hubert Fournier's side from European competition.