The 27 year old struck late on after an error from Salvatore Sirigu to steal a point for the bottom side and dent the visitors' title hopes.
Nene had put the visitors ahead midway through the first half with a wonderful virtuoso goal to seal his 14th strike of the campaign. Auxerre ramped up the pressure in the second half, and were ultimately rewarded with Anthony Le Tallec's late finish.
Carlo Ancelotti opted to re-introduce Kevin Gameiro to the starting line-up along with Mathieu Bodmer for the suspended Mohamed Sissoko as Javier Pastore was relegated to the bench Auxerre meanwhile, broght n Olivier Kapo for Roy Contout.
Les Parisiens, buoyed by the news that Rene Girard's men had lost 2-1 to Lorient earlier in the day started much the brighter against Jean-Guy Wallemme's beleagured side with Gameiro going close with an early opportunity.
Gameiro's exquisite back-heel in towards Jeremy Menez saw the ex-Roma winger collect the ball and inexplicably fired into the side-netting after going past Olivier Sorin. The hosts were equally lucky not to have been penalised after Stephane Grichting had tripped up Gameiro, though referee Jean-Charles Cailleux waved away weak appeals.
Auxerre's luck, however, had run out in the 23rd minute. Gameiro, making his first start in three weeks played a lovely ball towards Nene who jinked past two defenders and fire a powerful effort past Sorin for his 14th goal the season.
The relegation strugglers failed to pose a serious threat, despite an abundance of opportunities up front, although they too would be left aggrieved after a penalty appeal was turned down.
Kenyan international Denis Oliech's run into the area was curtailed by Milan Bisevac's outstretched leg, but replays suggested it was out of the box amidst outcry from the home faithful as the sides entered the half with Ancelotti's men leading.
The second half would prove to be a much more enterprising affair, and Menez would again see a chance thwarted seconds after the re-start which saw Sorin gather his dangerous effort at the second attempt.
Wallemme's side spurned their best opportunity of the match just before the hour mark. Kamel Chafni's run past Bisevac saw him strike the left post with Salvatore Sirigu well-beaten. Minutes later, they would be denied again.
Cedric Hengbart whipped in a timely cross from the left which was met by Oliech whose header was saved at point-blank range by Sirigu after an awkward bounce as Auxerre stepped up their efforts to equalise.
The capital club were noticeably lethargic in the second half despite only holding a slender lead. Menez was once again the guilty party after he failed to find Nene allowing Sorin to gain possession of the ball before Bodmer also was denied a goal from close range.
Sirigu would be worked once more, and was almost caught out by a freak effort from Georges Mandjeck. A speculative cross from the Cameroonian dipped alarmingly towards goal, leaving the 25 year old Italian to hurriedly tip the ball over the bar.
Auxerre were by far the better side and finally, their perserverance paid off. A fierce strike from Kossoko was spilled by Sirigu leaving fellow substitute Le Tallec to fire into an empty net as a furious Ancelotti berated his side at full-time.
Following on from the result, PSG remain second, two points behind Montpellier and host Sochaux next week. Auxerre remain rooted to the bottom, and next face fellow strugglers Nice in a vital clash.