Auxerre last won the cup in 2005 and players such as Eric Cantona, Djibril Cisse, Bacary Sagna and Enzo Scifo were once on the books of the now second-tier outfit.
Neupocoussek Mendy and Karim Tlili got the goals as the French Riviera minnows enjoyed their greatest exploit.
Top-flight Angers also go into the hat for the quarter-finals after a 1-0 win at third-tier CA Bastia in Corsica while Bordeaux beat Lorient 2-1 in an all top-flight clash.
Marseille play Monaco on Wednesday while champions PSG travel to second-division Niort on the same night.
