Second half goals from Ryan Croasdale and Matt Dudley gave PNE the points.
Burnley lead the table with 39 points from 16 matches after a 1-0 win at Shrewsbury.
Preston are one point behind the Clarets but have played one match more.
Walsall are third with 37 points from 15 matches. Walsall beat Morecambe 6-1 over the weekend.
Carlisle are fourth with 34 points from 17 matches.