Cameroonian striker Steve Mbida scored the only goal of the game in the first half as the fourth-tier outfit stunned last season's semi-finalists.
Christian Gourcuff's side were unbeaten in seven games before their trip to Stade de Bellevue, but they fell at the first hurdle in the cup to come crashing back down to earth.
Monts d'Or Azergues were another CFA club to upset the odds on Saturday as they beat Ligue 2 side Istres 3-2 on penalties.
Former France midfielder Ludovic Giuly put the amateur side in front and although Cheick Fantamady Diarra equalised in the second half, the minnows were not to be denied.
Bagaliy Dabo and Benjamin Mas missed from the spot after the two sides were locked at 1-1 after extra-time.
Valenciennes and Rennes also needed a penalty shoot-out to decide the only all-Ligue 1 tie on Saturday, with the latter coming out on top.
Julien Feret scored from the spot just after the hour mark to put Rennes in front, but Mathieu Dossevi pegged the home side back and the tie finished 1-1 after extra-time. It was Rennes who held their nerve to progress by winning the shootout 8-7.
Martin Braithwaite scored a last-gasp winner as Ligue 1 side Toulouse made hard work of beating Romorantin 2-1, while top-flight side Sochaux had no such trouble as they won 3-0 at Bressuire.
Ligue 2 Lens scored three times in the last nine minutes to win 3-1 and avoid an upset after CFA side Avranches had taken the lead.
There was heartbreak for CFA 2 side Aubagne as Florin Berenguer struck in the last minute of extra-time for Dijon to make it 3-3 and the visitors went on to win 5-4 on penalties.
Angers also triumphed in a shootout at Chambly, while Cercle Athletique Bastia beat La Roche-sur-Yon 3-0 after extra-time.
Moulins hammered Magny Renaissance 6-1, while Niort, Caen, Plabennec, Concarneau and Boulogne are all through to the next round.
The ties between St Etienne and Cannes and Jura Sud and Creteil were postponed.
