The victory put the Burgundy side a point ahead of Bordeaux, who slumped to their first home Ligue 1 defeat in over two years when Valenciennes beat them 1-0.
Mali defender Adama Coulibaly headed home a Benoit Pedretti free kick to put Auxerre in front just before half-time and Congolese midfielder Delvin Ndinga wrapped up their seventh consecutive win with a late goal.
Auxerre, French champions in 1996, have not been in the lead since February 2003. They have 26 points from 13 games, one more than Bordeaux and Olympique Lyon, third on goal difference after a 1-1 draw at bottom club Grenoble.
"First place at this stage doesn't mean much but we're happy with the three points," Auxerre goalkeeper Olivier Sorin told French television channel Orange Sport.
"This is great for us and for our fans. I don't know how long we'll stay there, probably not for ever but it's nice."
Bordeaux had not lost before their fans since a 3-1 defeat by Olympique Lyon in October 2007.
VERY FRUSTRATING
Forward Mamadou Samassa scored the winner for Valenciennes with an angled shot on six minutes, sending the northerners up to fourth, three points off the pace.
Bordeaux, who were missing key players in playmaker Yoann Gourcuff and holding midfielder Alou Diarra, both sidelined with injuries, lost their second league match in succession after a 2-0 defeat at Lille.
Coach Laurent Blanc would have hoped for a better warm-up before the team from the wine capital entertain Juventus in the Champions League on Wednesday.
"It's a long time since we played good football," Bordeaux defender Marc Planus told reporters. "We really tried tonight but couldn't make it. It's very frustrating."
Lyon were widely favoured to win at Grenoble, who had picked just one point from 12 games, and looked set to do so after Argentine winger Cesar Delgado put them ahead on 66 minutes.
Grenoble then had midfielder Laurent Courtois sent off in the 71st minute for angrily throwing the ball at an assistant referee. Two minutes later Serbian forward Danijel Ljuboja earned the home side a share of the points.
