Third-placed Lyon, who hold the final Champions League qualifying spot, were undone by Anthony Limbombe's late free kick after Martin Terrier had cancelled out Kalifa Coulibaly's opener for Nantes.
Lyon are on 56 points with six games left, six ahead of fourth-placed St Etienne, who play their game in hand at home against Girondins de Bordeaux on Sunday.
It was Lyon's third straight defeat in all competitions after they were knocked out of the French Cup semi-finals by Stade Rennes and lost at home to lowly Dijon in the league last weekend.
The result leaves an even bigger question mark over coach Bruno Genesio's future, with the club set to make a decision on whether to extend his contract at the end of the season.
With Nabil Fekir, Memphis Depay and Marcelo on the bench, Lyon got off to a bad start.
Coulibaly opened the scoring in the 11th minute after collecting a though ball from Majeed Waris.
Lyon were shaken by the hosts but weathered the storm and equalised one minute before the interval when Terrier curled a fine shot into the back of the net to finish off a counter attack.
Limbombe earned Nantes victory seven minutes from fulltime with an inch-perfect free kick, lifting the Canaries up to 15th in the table on 34 points.
(Reporting by Julien Pretot; Editing by Toby Davis)
