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."
"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."
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.
