Neil pushed Alan Browne up to the No.10 role and had Daniel Johnson slightly deeper than of late, with Ben Pearson playing the holding role.
On the right flank, Brad Potts made his first start since the League Cup tie with Manchester City a month ago, with Tom Barkhuizen on the left.
Barkhuizen put PNE 1-0 up in the 74th minute, scoring his fifth goal of the season from substitute Sean Maguire's cross.
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Leeds pulled level 13 minutes later through England Under-21 international who is on loan from Arsenal.
North End boss Neil said: "I knew we weren't going to dominate the ball because Leeds don't allow you to do that.
"If we'd had played DJ up there, it would have been a thankless task for him.
"So we needed Alan Browne's energy, someone to pick up second balls, run beyond David Nugent and stretch the game that way.
"I thought Alan did that very well.
"We played a six, eight and 10 really in midfield - DJ stretched Mateusz Klich one way and then matched him going the other way
"Brad Potts came in to help us counter-attack. What Pottsy is very good at is running from deep and getting into space.
"If you ask him to play as a winger with his back to goal, that is not his strength.
"I just thought we needed to change it for this game and it worked."