Nene's opener was cancelled out by Anthony Le Tallec three minutes from time after the Brazilian threw away a couple of clear chances to make it 2-0 for PSG.
Montpellier, who slumped to a sobering 2-1 defeat at Lorient stayed top on 66 points, two ahead of PSG, with six games left.
Titleholders Lille have 59 points, six ahead of fourth-placed Olympique Lyon before the seven-times champions' trip to Toulouse on Wednesday.
They now trail PSG by five points after the capital side failed to hold on to their one-goal lead.
"We can't play like that if we want to win the title. We need to defend with more character," PSG coach Carlo Ancelotti told a news conference.
"I'm angry at the players. We missed out on a great opportunity."
Ancelotti's late changes, however, were debatable as he replaced striker Kevin Gameiro with midfielder Javier Pastore and Diego Lugano came on for Mathieu Bodmer, leading to a reshuffling of the defence.
PSG played a good first half and were rewarded after 23 minutes when Nene burst into the area and whipped the ball past Olivier Sorin.
Auxerre increased the pressure after the break and Kamel Chafni came close on 53 minutes but his angled shot smashed Salvatore Sirigu's right post.
Sirigu then pulled off a lightning quick save to parry away Dennis Oliech's header on the hour.
Nene twice had the chance to double PSG's tally but opted for some fancy dribbling instead of firing home.
It was, however, Le Tallec who found the back of the net after Oliech's shot was deflected on to the post by Sirigu and into the path of the former Liverpool striker who tapped the ball into the empty goal.
Earlier, Montpellier suffered only their second Ligue 1 defeat in 2012.
Lorient got off to a solid start and had several early chances through Jeremie Aliadiere and Yann Jouffre.
Montpellier, however, upped the pace before halftime.
John Utaka collected a defence splitting pass from Giroud but he was denied by Fabien Audard. Giroud's delicate chip also went just wide.
Lorient then struck when Aliadiere's header bounced off Bedimo's head into the net in the 69th minute.
Montpellier were clearly unsettled and conceded a second seven minutes later when Costa Rica's Campbell curled a shot past Geoffrey Jourdren.
Giroud, the league's top scorer, soon pulled one back but Lorient held on.
"We were complacent. This defeat will bring us back to earth," Giroud told French TV channel Canal +.
St Etienne moved up to fifth on 50 points after Max Gradel and Bakary Sako's goals earned them a 2-1 win against visitors Stade Brest.