A penalty from Naim El-Harrati just before half time and a Sam Osobe in the 87th minute gave PNE the three points and the title by one point over Burnley.
Burnley had beaten Stockport 3-0 to finish the season on 58 pts but finished second to PNE who got 59 pts. Walsall are third with 51 pts with one to play.
Next Wednesday is the LFA Youth Cup Final as PNE try to retain the trophy against rivals Burnley at Deepdale.