Auxerre survived a major scare to book its place in the Coupe de la Ligue round of 32, as it was forced to go to penalties to see off Championnat National side CA Bastia.
The Corsican side was the last representative of the third tier left in the competition and stunned last season's Coupe de France finalist by taking the lead through Adama Guidiala with just eight minutes on the clock.
The visitor levelled on the stroke of half-time, however, courtesy of Pierre Bouby and eventually prevailed 3-0 in the shootout.
The clash between Bourg-Peronnas and Nancy also went to spot-kicks after the two sides had failed to produce a goal between them in 120 minutes, with the former ultimately squeezing through 5-4.
Unbeaten Ligue 2 leader Metz, meanwhile, slumped to a surprise 2-0 defeat at Dijon, goals from Mamadou Thiam and Lois Diony proving enough to send the 1996 winner tumbling out of the competition.
Tours also secured a 2-0 home win at the expense of Sochaux, with both of its goals coming in the second-half from Haris Belkebla and Christian Kouakou.
Evian held off a late charge from Clermont to progress 3-2 at the Parc des Sports d'Annecy.
Goals from Fabien Centonze, Hernan Altolaguirre and Aaron Appindangoye had put the recently-relegated host 3-0 up early in the second half, but late replies from Wesley Jobello and Idriss Saadi set up a tense finale.
The clash between AC Ajaccio and Laval was also a tight affair, with the visitor eventually edging it 2-1 thanks to a Rachid Alioui effort three minutes from the end of extra-time.