North End dominated the opening 45 minutes but went in goalless at the break before Scott Medlan and Tom Croughan scored for Tranmere in the second half.
The visitors made a positive start to the game as Mike Howard intercepted a header back to goal by controlling with his chest and volleying goalwards, only for the Tranmere ‘keeper to tip his effort just over.
Josh Earl found the net for the Lilywhites but his header from Melle Meulensteen’s corner was disallowed in the eighth minute.
Ki Smart then volleyed narrowly wide after a corner was cleared before goalkeeper Callum Roberts held on to Ethan Devine’s drive from outside the box at the other end.
Croughan then hit the post for the home side close to goal but PNE continued to attack as Meulensteen curled one over from just inside the box midway through the first half.
Earl had his shot from outside the box saved before heading narrowly wide from a corner in the following moments.
The visitors continued to push and Howard went close again just before half-time when the ball bounced up invitingly in front of him, but his half-volley flashed just over the bar.
Meulensteen also narrowly missed with a curling effort before the end of the half, and with the scores level at the break, PNE came out just as strong at the start of the second half.
Smart and Earl put efforts over and wide respectively from Meulensteen’s early second-half free-kicks before Tranmere started to create more chances of their own.
Jack Burgoyne brilliantly headed away a dangerous cross at point-blank range to keep the home side
Tranmere attacked down the right side as a loose ball fell to Medlan, who headed in from the other side of the box after 63 minutes.
Roberts made a couple of excellent saves to deny Tranmere’s Croughan later in the half while Tom Barry and Harry Garstang came on for PNE.
The latter almost pulled one back for the visitors with only eight minutes remaining, as he turned and shot from the edge of the area, only to see his effort saved at the bottom left corner.
Left-back Earl led PNE’s pursuit of bringing the scores level as he surged down the left flank several times in the final minutes, but those attacks came to nothing as Barry had one shot blocked before another dangerous delivery went right across the six-yard box.
Tranmere scored their second in the 90th minute as Tom Croughan received a pass on the right side of the area and shot into the bottom corner to double his side’s advantage.
The game ended as a 2-0 defeat for the Lilywhites and academy boss Nick Harrison was disappointed to lose after his players had impressed him with their first half display: “I thought we were very good in the first half and I think we had a couple of goals disallowed which should have stood.
“If we had gone into the second half 2-0 up it becomes a different game and we would have played differently as opposed to it being 0-0.
“We told the players that they were excellent in the first half and asked them to carry on with what they were doing, because what they were doing was very good.
“We’re really disappointed to have lost the game. In the second half, we made some poor decisions on the ball, lost possession in key areas and didn’t defend well.”
When asked what changed after the break, Nick explained: “We had to make a change at the back because of injury, so we could maybe put it down to that.
“In the first half I felt like we defended and attacked well as a team and made good decisions on and off the ball, but we just didn’t do that at all in the second half.”
Despite that, Nick believed his side did enough to win the game but stressed the importance of the players taking their chances: “We created enough chances throughout the game to win it – there’s no doubt about that. We had as much possession as them and had more chances on goal.
“It doesn’t matter how many chances you create, though, it’s about putting the ball in the back of the net and keeping it out of your net.
“We missed some good chances to score and didn’t defend well enough as individuals or as a team to stop them from scoring.”
Nick is now keen to see a repeat of the first half performance in upcoming matches: “If we play like we did in the first half for the full 90 minutes then we’ll have a chance of winning games.
“We’ve got to score goals and keep clean sheets and I see no reason why we can’t do that.
“We’ve got players who are capable of doing that but they’ve got to do it when they’re under pressure and there’s an opposition trying to do the same.
“It was definitely a game of two halves. We really dominated the first half without scoring a goal but the second half was completely different and we’re disappointed with that.”