Melle Meulensteen put the visitors ahead from the penalty spot on 64 minutes before PNE took advantage of the hosts being reduced to ten men as Akwasi Kwateng and Alex Wood struck late on.
North End started well and might have scored inside the first minute as Mike Howard controlled a long pass and raced past his marker, but he placed his shot just wide of the post.
John McAtee missed a couple of chances at the other end for the hosts as the visitors held firm at the back in a new-look 3-5-2 formation.
Meulensteen then narrowly curled over the bar from a North End free-kick minutes before Callum Roberts held onto Charley Higgs’ header at the other end.
The Lilywhites then had Josh Earl to thank for clearing off the line midway through the half, and Shrewsbury were then denied by the crossbar from a corner minutes later.
Roberts made another terrific stop to deny McAtee one on one soon after but North End remained a threat at the opposite end, as Tom Barry saw his left-footed volley well collected by the opposition goalkeeper 10 minutes before the break.
The first half finished goalless as the two sides battled for superiority in the middle, and the game continued in a similar fashion after the break until Howard’s persistence earned North End a chance 10 minutes after the restart.
Shrewsbury’s defender couldn’t cope with Howard’s intense pressing as the forward stole possession deep on the right flank and tested the ‘keeper with a vicious strike.
Meulensteen then replicated Howard’s relentless run as he regained the ball on the left side and crossed for Oscar O’Neil on the edge of the box, with the midfielder poking a shot just wide.
Akwasi Kwateng and Alex Wood were introduced on the hour as O’Neil raced forward and shot wide of the near post from just outside the box.
The breakthrough came in the 64th minute when Earl was unfairly held in the box, resulting in a PNE penalty which Meulensteen confidently placed down the middle.
Shrewsbury’s Ryan Sears was then shown a red card for his last man challenge on Howard, who had made another dangerous run towards goal.
The home side pressed for an equaliser but the Lilywhites’ remained comfortable at the back while maintaining their threat going forward, which nearly brought a second goal 10 minutes from time when O’Neil headed just over from Earl’s perfectly placed left-wing cross.
PNE did double their lead in the 83rd minute when Howard found Kwateng, who showed remarkable composure to take it past his man inside the box before firing into the roof of the net.
That gave the visitors added confidence and Meulensteen nearly got his second a minute from time after latching onto Howard’s flick-on, but the captain’s low placed effort was well saved.
Kwateng and O’Neil saw efforts blocked before Wood curled one over in the final moments, but the latter did get on the scoresheet late in added time.
Meulensteen had another shot parried by the goalkeeper but Wood was in the perfect position to tap in from close range, earning PNE a fantastic 0-3 away victory.
Academy manager Nick Harrison was pleased with the result, saying: “We’re delighted to win and we think it’s been coming over a number of games.
“We’ve drawn a lot of games where we probably could have nicked a win.
“I thought the lads were very good, especially in the second half, and thoroughly deserved to get the win and the three points.”
When asked about the change of formation and his team’s performance in the system, Harrison added: “It’s all about development for the players and it’s important that they know how to play in a number of formations.
“We’ve worked with a couple already this season and we wanted to see how the boys could cope with another change of system. It’s something that the first team play so if they’re going to progress they will have to deal with that.
“I thought everyone played their part within the game and in the formation, but it was just the principles of the game that we were more pleased with.
“We worked hard, passed the ball better – especially in the second half, and provided more of a threat on goal."
However, Harrison did not believe the formation was the reason for the clean sheet. He said: “The clean sheet was down to the players making better decisions on and off the ball maybe than they have done in previous games.
“I thought we made better decisions today which is why we kept a clean sheet and scored the three goals. We defended much better as a team.”
Harrison also explained what he asked of his players at the break before the three goals followed in the second half. He added: “When we passed the ball in the first half we felt we opened them up and got more success.
“We did that even better in the second half which is why we ended up winning the game 3-0, and it could even have been six or seven with the chances we had towards the end.”