Midfielder Jeremy Clement headed home a cross by Brazilian defender Ceara on 67 minutes to give PSG the points and move the capital club up a spot to 12th in the 20-strong league.
The Auxerre players shouted for a penalty seconds after the goal when striker Roy Contout was brought down by PSG defender Mamadou Sakho but the referee ruled the offence was committed outside the box.
"This leaves a bitter taste because it was definitely a penalty," Auxerre coach Jean Fernandez told reporters. "It's really a pity to see our strong run end this way."
PSG lost goalkeeper Gregory Coupet, who left the pitch on a stretcher six minutes from time after twisting his leg while trying to prevent a corner. He was taken to hospital with a suspected broken leg.
"We should be celebrating but Gregory's injury ruins it," PSG president Robin Leproux told reporters. "We are almost certain that he has a left-leg fracture. It's a shock because Gregory is very important to our team."
Lorient moved into second place, also a point off the lead, after needing a goal in added time from forward Kevin Gameiro to salvage a 2-2 home draw with bottom club Grenoble, still without a win after 14 games.
In a late game, seventh-placed Olympique Marseille lost 1-0 at strugglers Racing Lens, with Brazilian striker Eduardo scoring the winner in added time.
Montpellier's squad has been hit by the H1N1 flu virus, forcing their Ligue 1 game at Monaco scheduled for Saturday to be postponed.
No new date has yet been set.
