The Brazilian attacking midfielder cancelled out Cedric Cambon's first-half opener and netted a penalty before Kevin Gameiro added the third one minute from time to give PSG 49 points from 22 games.
"We really fought after the break because our first half was bad," Nene told French TV channel Foot Plus.
"I'm happy to score, but just because it helps the team."
Second-placed Montpellier kept pace after Geoffrey Dernis gave them a 1-0 home victory against Stade Brest.
The Saint-Etienne v Lorient game was abandoned after only 10 minutes because of a frozen pitch.
It was also below freezing at the Parc des Princes but the game went ahead, although it took more than 45 minutes for PSG to warm up with Italy midfielder Thiago Motta making his debut.
Evian took a 1-0 lead into the break after Cambon headed home from close range but PSG, who have won their three league games under new coach Carlo Ancelotti, piled on the pressure in the second half.
Nene was set up by Jeremy Menez just outside the box and slalomed through the defence before beating Stephan Andersen.
With 11 minutes left, Menez was tripped in the box and Nene converted the resulting penalty, with Gameiro putting the result beyond doubt in the 89th minute with his first league goal in almost two months.
Montpellier still trail PSG by three points after edging past Brest.
Remy Cabella's shot took a deflection off Dernis's back into the net six minutes before the break and it was all Montpellier needed to secure their third successive Ligue 1 win.
Stade Rennes remained sixth on 36 points after a goalless draw at Nancy while Toulouse, in seventh, lost 2-0 at Girondins Bordeaux.
The hosts took a first minute lead through Brazilian Jussie and added a second five minutes before the break courtesy of Ludovic Obraniak. Toulouse were reduced to 10 men three minutes before the break when midfielder Moussa Sissoko was sent off.
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