The Lilywhites enjoyed fast starts to both halves, scoring both of their goals as they came quickly out of the blocks.
Tom Barkhuizen opened the scoring after a sensational pass from Ben Pearson found Daniel Johnson, who then laid it on a plate for the winger.
It was roles reversed in the second half, with Barkhuizen finding Johnson, who took a touch and dispatched the ball into the corner.
Chey Dunkley halved te deficit shortly after and PNE had to battle to keep in the lead, and send themselves into the play-off places, where they will stay for this round of games.
Paul Cook, who was booked during the game, was not impressed with his Wigan side and felt the second goal was the killer.
He said: "It was in general as flat and as poor as we’ve been for quite a period time, we didn’t have enough players winning individual battles all over the pitch.
"It took about until the last 25, 30 minute until the young and came off the bench to give us a real spark, where we then huffed and puffed and took semblance of credit out of the game.
"The game had gone away from us with the second goal, great credit to Preston.
"You’ve got to accept sometimes, I thought Preston were better than us for long periods of the game and in my opinion deserved the win.
"Preston started the game with more intensity, they started in more positive positions on the pitch than us. We didn’t track runners, we weren’t aggressive.
"We pat Preston on the back and say well done, they’re a very good side.
"He’s a top manager (Alex Neil), he’s a really good manager in this division for sure, and probably in the division above.
"They will go onto what they’re pursuing and we’ll go onto ours."