The home side opened the scoring ten minutes into the second half with highly-rated defender Philippe Mexes netting.
Jet-heeled striker Djibril Cisse doubled the lead after 64 minutes to give Auxerre all three points and frustrate Didier Deschamps' men.
Elsewhere, Bastia beat Troyes 2-0, through goals from Tony Vairelles and Ousmane Soumah - after Frederic Danjou had been sent off for the visitors.
Cedric Bardon's strike six minutes after the break gave Guingamp victory over Lens.
Marseille came from behind to beat Lorient 3-2. Jurgen Cavens opened the scoring for l'OM, and after Seydou Keita and Pascal Feindouno netted for the visitors, Jerome Leroy and Moreira Andre Luis netted to give them victory.
Montpellier also recovered from a deficit to beat Nantes 2-1. Victor Bonilla put Nantes ahead on the hour mark, but Franck Silvestre and Fode Mansare both scored to give Montpellier victory.
Finally, Sedan and Rennes played out a goalless draw.
Click on fixture for full match summary
Auxerre 2-0 Monaco
Bastia 2-0 Troyes
Guingamp 1-0 Lens
Marseille 3-2 Lorient
Nantes 1-2 Montpellier
Sedan 0-0 Rennes
