Fekir struck in the 35th minute after Felix Eboa Eboa had cancelled out Martin Terrier's opener to put Lyon on 46 points from 25 games.
Lyon, who host Barcelona in their Champions League last-16 first leg on Tuesday, trail second-placed Lille by three points having played one more game.
Leaders Paris St Germain, on 59 points from 22 games, travel to fourth-placed St Etienne on Sunday.
Bruno Genesio's side went ahead in the 15th minute when Marc-Aurele Caillard parried Houssem Aouar's shot into the path of Terrier, who volleyed the ball into the top corner.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
The hosts, however, let their guard down and Eboa Eboa headed home six minutes later.
Lyon took the upper hand 10 minutes from the interval as Fekir chested the ball down in front of the area and unleashed a perfectly curled shot past Caillard.
(Reporting by Julien Pretot; Editing by Pritha Sarkar)
