Paul Baysse's 17th-minute opener had set the hosts on their way to inflicting a first defeat of the season on the principality side before Alassane Plea rounded off a successful evening for Les Aiglons late on.
Bordeaux climbed into fourth place with a 3-0 victory at Metz.
Brazilian forward Malcom gave Les Girondins the lead after 37 minutes. Gaetan Laborde doubled the visitors' lead in the second half before Kiese Thelin's penalty five minutes later sealed all three points.
Nabil Fekir and captain Corentin Tolisso both scored twice as Lyon came from behind to beat 10-man Montpellier 5-1.
Morgan Sanson gave the visitors the lead after only four minutes but four minutes later 19-year-old debutant Morgan Poaty was sent off for a challenge on Tolisso.
Lyon were ahead by the break through a Fekir penalty and one from Tolisso and the pair both scored again in the second half before Maxwel Cornet added a fifth.
Ten-man St Etienne held on to secure a point at Nantes in a goalless draw at Stade de la Beaujoire.
In an eventful first-half, the visitors made three substitutions in the first 21 minutes and were reduced to 10 men when substitute Kevin Malcuit was shown a red card for a foul on Alex Kacaniklic moments after his introduction.
But Emiliano Sala missed the resulting penalty as the hosts failed to make the most of their chances.
Angers defeated Caen 2-1 to make it three wins in a row after losing their opening three.
Billy Ketkeophomphone and Cheikh Ndoye put them two up and Yann Karamoh's second-half strike proved to be only a consolation for Caen.
Jimmy Briand scored the only goal as Guingamp saw off bottom side Lorient while Nancy held Bastia to a goalless draw.
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