Lyon missed out on a chance to seal a Champions League last 16 place with a match to spare after losing 2-0 at Zenit Saint Petersburg on Wednesday.
A victory in Group G over the Russian Premier League leaders would have claimed a knockout spot for Rudi Garcia's men.
Lyon are now third behind Zenit, level with the Russians on seven points, ahead of their final group match on December 10 against leaders Leipzig, who are three points clear at the top and assured of a place in the knockout round.
"Lyon are a really good team. But we were prepared well and did what we had to," Zenit midfielder Magomed Ozdoev told UEFA.com.
"Now it's all about the match in Lisbon and we will be ready for it."
Bundesliga side Leipzig's last-gasp 2-2 draw with Benfica later in the day gave them a place in the last 16 for the first time leaving Lyon and Zenit in pursuit of the second qualifyng spot.
"It's not over, we still have our last match to play and we're supporting Benfica (who face Zenit in the last round)," Garcia said.
"What is certain is that we have to beat Leipzig, who I think are the best team in the group."
Zenit coach Sergei Semak kept faith in the starting lineup from the weekend's 2-1 league victory over Rubin Kazan, with Artem Dzyuba who scored that winner in that game leading the attack.
Garcia, who replaced the sacked Sylvinho in October, was without injured midfielder Thiago Mendes and ill winger Martin Terrier after beating Nice on Saturday as 16-year-old attacking midfielder Rayan Cherki was named on the bench.
- Ill-disciplined Lyon -
The best of the early chances fell to Sardar Azmoun on 35 minutes after Daler Kuzayev and Joachim Andersen were shown yellow cards in the opening half an hour.
Iran forward Azmoun, broke through the French defence but his chipped shot hit the post before he was brought down by Anthony Lopes, with VAR deciding against awarding a penalty.
Dzyuba went one better than Azmoun seven minutes later to claim a lead for the Russian outfit.
The Russia international headed in from a Douglas Santos corner as Lyon protested with referee Daniele Orsato for Dzyuba's tussle with Marcelo in the penalty area.
Captain Leo Dubois and fellow-wing back Marcal were shown yellow cards by Orsato for their complaints.
Semak's men controlled a lacklustre second-half and Ozdoev made sure of all three points with his third goal of the season in the 84th minute.