Bruno Genesio's men eased to their second victory from as many league home matches this term thanks to goals from Martin Terrier and Bertrand Traore, while Fekir, who saw a move to Liverpool fall through in the close season, played the last 11 minutes.
The home side took the lead shortly before half-time as full-back Ferland Mendy slipped through an inch-perfect pass for Terrier, who spent last season on loan at Strasbourg, to curl into the bottom corner.
Former Chelsea forward Traore wrapped up the win in style with a fantastic individual goal in the 64th minute, latching onto Memphis Depay's ball before dribbling past visiting goalkeeper Matz Sels and a backtracking defender to slot in.
Fekir missed the first two games of the season after returning late from the World Cup, where he made six substitute appearances in France's triumphant campaign.
Lyon, who finished third last season to qualify for the Champions League group stage, have now won their last eight home Ligue 1 matches.
Reigning champions Paris Saint-Germain welcome Angers to the Parc des Princes on Saturday, when new coach Thomas Tuchel could field forwards Edinson Cavani, Neymar and Kylian Mbappe together for the first time.