Fekir, who is still undecided on whether to represent France or Algeria internationally, struck in the 67th minute to put Lyon on 54 points from 26 games.
"It was an important game after Paris won yesterday. It was not perfect but we're back on top and we're happy," Fekir told BeIN Sport.
Lyon lead second-placed Paris St Germain, who beat Toulouse 3-1 on Saturday, by two points.
Olympique de Marseille are third on 50 points after Mevlut Erding's injury-time goal salvaged a 2-2 draw for hosts St Etienne.
Les Verts are fifth on 42 points.
Lyon welcomed back Ligue 1 top scorer Alexandre Lacazette, who had been out of action since pulling a hamstring last month.
Lacazette, who has scored 21 league goals this season, was substituted in the 67th minute, just after setting up Fekir for the only goal.
Fekir poked the ball home from close range after his curled free kick had hit the woodwork five minutes before the interval.
Fekir has nine goals and six assists to his name this season.
Lyon dominated throughout and were greatly helped by playmaker Yoann Gourcuff, who initiated the move that led to Fekir's goal.
Nantes's biggest chance came in the 29th minute when Serge Gakpe's strike shaved Anthony Lopes's post.
The Canaries, who lie 11th in the table on 33 points, have not scored an away goal since Dec. 20.
They could have conceded another one in added time but Maxime Gonalons missed a penalty awarded after Fekir had been brought down by keeper Remy Riou.
(Reporting by Julien Pretot, editing by Pritha Sarkar)
Share
