Augusto Fernandez and Ilan found the back of the net in the first half as champions Bordeaux, who were without France playmaker Yoann Gourcuff through injury, struggled to find their rhythm.
Brazilian forward Jussie converted a 69th-minute penalty to reduce the arrears but substitute Dimitri Payet added a third in stoppage time as Bordeaux conceded their first defeat in all competitions from 23 matches.
"We are very disappointed, but it happens, we knew we would not be unbeaten all season," Bordeaux keeper Cedric Carasso told French TV channel Foot Plus.
Second-placed Olympique Lyon, who are two points adrift of Bordeaux, will have the opportunity to claim the lead when they travel to RC Lens later on Saturday.
Promoted Montpellier moved up to third as they snatched a 3-2 win at bottom club Grenoble, who have now lost all their eight games this season in the worst start to a French top-flight season.
Benin midfielder Stephane Sessegnon salvaged a 1-1 home draw for Paris St Germain against Nancy but the capital side, fifth in the standings, have now failed to win in their last four league games.
Stade Rennes were down to 10 men after only 16 minutes when Carlos Bocanegra was sent off and lost 1-0 home to AJ Auxerre to slip to sixth.
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