Ligue 1's fourth-placed side was undone in the 92nd minute by a team 15th in the Championnat National as Mathieu Geran netted a dramatic winner for Entente.
Also tumbling out in what is officially the ninth round but the first hurdle for Ligue 1 clubs were Angers and Nimes.
Angers lost 1-0 to sixth-tier Viry-Chatillon while Nimes was thumped 3-0 by Lyon Duchere of the National. Meanwhile, Lyon came through a testing encounter with fifth-tier Bourges 2-0.
Caen survived against Ligue 2 Red Star, prevailing 1-0, while Amiens beat Valenciennes by the same scoreline. Dijon overcame Schiltigheim 3-1 and Guingamp came from behind to beat Stade Pontivyen of the fifth tier 4-2.
Martinique's Aiglon du Lamentin, the last team from outside France left in the draw, lost 3-2 after extra-time to Ligue 2 Orleans.