Fekir was taken off at half-time during the Ligue 1 derby clash against Saint-Etienne on Friday with an adductor injury, sparking concerns he could miss the midweek Group F game with Pep Guardiola's City.
But the France international said: "Everything is fine, I'm recovering.
"We had some trouble in the first half but the most important thing is the victory. I'll be there on Tuesday."
Lyon warmed up for the visit of the Premier League champions with victory in the Derby du Rhône, to go second in Ligue 1.
Jason Denayer, the ex-City defender, headed the winner after 62 minutes but they rode their luck for much of the game.
Anthony Lopes kept out Lois Diony and Mathieu Debuchy in the first half and though Rafael da Silva was sent off with 20 minutes to go, the hosts held on.
And Belgium international Denayer hopes his side can take that momentum into the clash with Guardiola's men.
"In recent days we started feeling that it was a different match with a special atmosphere," he said.
"I didn't really think about scoring before. It's a lot of fun.
"Antho (Lopes), this isn't the first time he's saved us. I hope it isn't the last, either.
"I hope we can continue this momentum. Manchester City will be different for me, too.
"We will do our best to win and get the three points."