The Lilywhites were very much second best in the first half, the Magpies deserving of their interval lead given to them by an early penalty from Josh O’Keefe.
Simon Grayson changed all the side at half-time - a planned exercise - and the second-half team changed PNE’s fortunes.
Joe Garner finished a Paul Gallagher cross to equalise, then Jordan Hugill got on the end of Ben Pringle’s free-kick to head the winner.
Victory saw them lift the Jack Kirkland Memorial Trophy which is played for by the two clubs on an annual basis.
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North End were in a 3-4-1-2 system for the first half, Liam Grimshaw, Paul Huntington and Ben Davies forming the back line.
Chris Humphrey and Greg Cunningham provided the width, with Ben Pearson and John Welsh in midfield.
Further forward, Daniel Johnson played behind front two Jermaine Beckford and Simon Makienok.
The visitors were caught out within 33 seconds by Chorley, slack defending allowing Sefton Gonzales to run into the box where he was bundled over by a combination of Huntington and Grimshaw.
Referee Michael Salisbury pointed to the spot, O’Keefe tucking the penalty past Chris Maxwell.
Gonzales and strike partner Marcus Carver were to continue causing the North End defences throughout the first half.
The Magpies had the better of the play, certainly in terms of the clearer chances created.
A shot on the turn from Jermaine Beckford which cleared the bar by some distance, was a rare chance for PNE in the opening 20 minutes.
Dale Whitham put a header wide of the back post after being found by Adam Blakeman’s searching cross from the left.
Gonzales curled a shot behind, the home side having broken forward on the counter-attack.
In the 23rd minute, Welsh’s pass was chased to the byline by Humphrey, his cross to the far post headed down by Makienok.
The ball fell to Cunningham whose first-time shot flew high over the bar without troubling Sam Ashton.
Grimshaw and Carver had to be separated after coming together following the Preston player’s block on the Chorley forward.
A quiet word from Mr Salisbury ended the incident which in a league game could have led to sterner punishment.
Chorley’s pressure continued with Gonzales volleying over, before the former Clitheroe man missed a golden opportunity to stretch the lead seven minutes before the interval.
Carver did superbly down the right channel, his cross presenting Gonzales with a simple chance in the middle which he put over the bar.
North End changed their entire team at half-time and twice in the first four minutes of the second period, had sights of goal.
Doyle chased a ball down the left, his low centre met by Hugill whose first-time shot dropped inches over.
Another cross from Doyle, this time from the right, found Garner with his back to goal.
He turned but struggled to get the ball out of his feet, eventually getting a shot off which went straight at keeper Ashton.
The improved show was rewarded in the 57th minute as the Lilywhites pulled level.
Ben Pringle played a shot corner on the right to Gallagher, his low cross into the box swept home first-time by Garner from eight yards.
Chorley had the chance to regain the lead almost straight away, Dale Whitham’s free-kick sailing across the box to find substitute Jordan Connerton unmarked.
But he could not get much power on his header and Anders Lindegaard held it under the bar.
North End went in front in the 64th minute, Pringle’s free-kick picking out Hugill at the far post whose downward header bounced back across goal and into the net.
There was concern for PNE with 10 minutes left when Tommy Spurr went down after appearing to twist his right ankle.
He was helped off by physio Matt Jackson, with Davies coming back on to replace him.
Soon after play re-started, Lindegaard was forced into a diving save from Jack Lynch’s shot..
Chorley: Ashton, Challinor, Blakemann (Beesley 58), Teague (Charnock 58), Leather, Jordan (Payne 67), Cottrell, Whitham (Roscoe 72), Carver (Connerton 46), Gonzales (Lynch 75), O’Keefe (Jarvis 58). Subs: Hartley, Nelson, Wood.
PNE (first half): Maxwell, Grimshaw, Huntington, Davies, Humphrey, Pearson, Welsh, Cunningham, Johnson, Makienok, Beckford.
PNE (second half): Lindegaard, Smith, Clarke, Woods, Spurr (Davies 80), Gallagher, Browne, Pringle, Doyle, Garner,, Hugill.
Referee: Michael Salisbury (Preston)