Goals from Sean Whelan and Adam James Robinson earned North End a place in the fifth round of the FA Youth Cup at St James Park.
The home side had taken a second half lead through Frank Rosenweld, after PNE had dominated the first half, but they showed great resilience to come back and equalise with a close range header from skipper Whelan and the winner right on the 90 minute mark from Preston-born Robinson, who had moved from midfield to attack in the closing stages.
North End had dominated the first half, Matt Hudson at times a mere spectator as the Academy played a high intensity pressing game that pinned the Grecians in their own half.
The only thing that would have concerned Academy staff Nick Harrison and Andy Fensome would have been the fact the young Lilywhites hadn't taken any of the plethora of chances they had created in what at times were testing conditions, with spells of both driving rain and snow adding to the already heavy St James Park pitch.
The chances started early for PNE, a fourth minute run from JJ Lunney from his own half before unleashing a shot from 25 yards, the ball palmed wide at full stretch by Exeter goalkeeper Kavanagh Keadell.
The home side stopper was a busy man in the first half, but he was a spectator as Dylan Davidson crossed from the right, the ball avoiding everyone before flying only a yard wide of the left hand post.
Lunney again collected right back and recent professional graduate Clive Smith's pass and fired hard and low, but impressive City centre half Jordan Storey blocked for a corner, from which Keadell did well on the line to prevent back heel from Earl scoring.
An effort from skipper Sean Whelan assisted by a Lunney free kick was cleared off the line after spill from Keadell and the follow up was poked wide by Adam James Robinson.
North End had strong penalty claims after Smith's 40 yard header into box for Freddie Tracey who was blocked off by Storey when seemingly in on goal.
However, Exeter made North End pay for those chances seven minutes into the second half when Frank Rosenweld capitalised on a short back pass straight into his path, sliding the ball under Matt Hudson and over the line despite the efforts of Jack Burgoyne to try and keep it out.
The rain became incessant after the hour mark with North End looking to make their attacks the same in an effort to draw level.
And the persistence paid off as North End drew level on 64 minutes. JJ Lunney's free kick into the box was headed goalwards by Sean Whelan and Keadell could only push it back out to the diminutive Irishman who headed back over the goalkeeper, off the bar and into the back of the net.
And they kept knocking on the door and as the clock struck exactly 90 minutes a free kick was played in by JJ Lunney, flicked on by Jack Burgoyne and Adam James Robinson slammed home from six yards out under Keadell.
Three minutes stoppage time was added on by the officials, but it was managed well by the young Lilywhites and they earned themselves a place in the fifth round against either Oldham Athletic or Luton Town at Deepdale.
Exeter City line-up: Keadell, Egan (c), Down, Merritt, Grimes, Storey, Smallcombe (Rehemi, 88), Hargreaves, Seymour, Richards (Collins, 60), Rosenwald. Subs not used: Williams, Rogers, Hartridge.
PNE line-up: Hudson, Smith, Whelan (c), Boyd, Burgoyne, A Jo Robinson, Davidson, A Ja Robinson, Tracey (Meulensteen, 62), Lunney, Earl (Jagne, 73). Subs not used: C Roberts, Crankshaw, Creech.
Referee: Mr A Ricketts