Despite the 2-1 defeat at the Juventus Stadium, Les Gones progress on the away-goals rule following the shock 1-0 first-leg victory in France back in March.
The two sides exchanged penalties in the first half, with Memphis Depay and Cristiano Ronaldo trading goals from the spot following dubious decisions. Ronaldo temporarily gave the hosts life with a stellar left-footed strike from distance just before the hour mark.
Depay opened the scoring with a Panenka from the penalty spot after Rodrigo Bentancur was alleged to have caught Houssem Aouar with a sliding challenge. On second viewing, it looked like a faultless tackle from the Uruguayan midfielder.
With the goal, Depay became just the eighth player in Champions League history to score in six successive matches.
Juventus resembled a side that had won just two of its last eight league outings, though they had their chances.
Karma swiftly repaid Maurizio Sarri's charges for the earlier controversial call, gifting the Old Lady a fishy penalty of her own minutes before the break.
Depay was accused of handling the ball minutes before the interval when Miralem Pjanic's free-kick struck the Dutchman in a three-man Lyon wall. Replays showed that Depay's arm was not in an unnatural position, but was draped by his side in a situation where the attacker could do little to avoid contact.
Juventus came out of the interval needing two goals to overturn the tie, and Ronaldo gave the hosts life with a preposterous strike from distance on his left foot that beat Lopes at the top corner with half an hour to play.
In the end, Lyon did enough to progress, relying on a 2-5-3 setup and some disciplined defending that allowed the visitors to sit deep and soak up pressure. It's quite the turnaround for Rudi Garcia's men after Lyon finished seventh in Ligue 1, nine points adrift of a European place.