Substitute Bafetimbi Gomis' second half strike was enough to give the French side victory at the Stade Gerland, enabling them to leapfrog Betis at the top of Group I.
While both sides are assured of a spot in the last 32, Lyon are desperate to clinch first place in the group, which they can do with a win over Vitoria Guimaraes in a fortnight.
"The qualification is the night's good news. It's been painful at times but we've got out of the group and we have to savour it," Lyon head coach Remi Garde said.
"We haven't won anything yet but the squad has been rewarded with this progress.
"We're representing French football here and the achievement shouldn't be played down.
"In the first half the distance between the lines was too great and we corrected that at half-time.
"Yoann and Bafetimbi coming on was important for us and I hope qualifying here will prove to be positive for the rest of the season to come."
Lyon skipper Maxime Gonalons added: "We all hoped before the game that we'd clinch qualification.
"That's the main piece of good news of the evening. We now have to go to Guimaraes to try and claim first place.
"We had difficulty imposing our rhythm on the game in the first half – we gave away possession a lot. The more the match went on, the better we felt. We stayed solid right until the end."
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