PNE were knocked out of the Premier League U21s Cup in cruel fashion with a last minute goal the difference in the tie.
North End had dominated for large parts of the game, but a dubious goal in the 90th minute saw an end to their cup campaign at the first hurdle.
It was second half substitute Daniel Hector with the breakthrough, he fired at goal, producing a fine save from Callum Roberts, before Clive Smith looked to hook it away before it crossed the line, but the referee gave the goal.
Despite being the one goal throughout the game, there were plenty of chances for both sides throughout the 90 minutes, but the game took time to get going.
There was little in the way of chances early on, with Doncaster coming closest in the opening ten minutes of the tie.
First it was through Paul McKay, when he met a free-kick played in by Whitehouse but Callum Roberts in the PNE goal did well to gather it.
Just at minute later, the hosts were on the attack again and won themselves a corner. It was swung in from the left and was met by Dany N'Guessan, but his header flew inches over the bar in what was the first real chance of the game.
On twelve minutes it was PNE on the attack this time, Andy Little almost capitalised when Rovers 'keeper Marko Marosi took too long to deal with a pass back, but the No.1 managed to clear just in time under pressure from the North End striker.
It was end to end for the remainder of the half, Roberts was called into action again to deny the hosts, before Sean Whelan provided a crucial block to stop the rebound.
Donaster were on the break again soon after, Lunney with a great ball deep into the box for PNE was punched clear by Marosi which started a counter attack from the hosts, but Whelan did well to cut out the danger down the right.
N'Guessan was causing all sorts of problems for the PNE defence in the first half, his driving run down the left was followed by a dangerous ball across the box, but Mandeville mistimes his volley and the danger passes.
It was N'Guessan with a powerful run down the left pace again, this time he fires at goal, but it was deflected twice before going out for a corner. The hosts were unable to capitalise on the set piece but continued to look for the opener.
Rovers then had two chances in quick succession before PNE started to put the pressure back on to the hosts.
Both came from Michael Carberry, who was first denied by a fantastic save from Roberts, after his shot deflected off PNE captain Josh Heaton.
The resulting corner fell to Carberry on the edge of the box, and he was this time denied by a goalline clearance.
North End then turned the tables in the final ten minutes of the half, piling the pressure on the hosts.
Andy Little stole the ball on the right before beating his man and bursting into the box, he tried his luck at goal but his effort went wide and into the side netting.
Soon after, it was Little again looking to get on the scoresheet. The corner in by Mulensteen was headed clear before it fell to Little, but the striker's speculative effort was mistimes and was subsequently cleared.
The hosts found themselves under increasing pressure and Nick Harrison's side may have felt disappointed to in to the break goalless.
Jonathan Lunney pulled the trigger with a powerful strike from the right, just outside the box, but it was pushed around the post for a corner.
Meulensteen stepped up to take it, the ball fell to Robinson, who layed it off to Heaton but the defender is denied by a great save from Marosi.
Just before the whistle went for half-time, there was a real let off for the hosts, as the ball pinballs around the Doncaster penalty area before the defence eventually clear it.
It was goalless at the break, but PNE certainly ended the half the stronger side, with a number of chances to take the lead.
Doncaster made two changes at the break, with John McKay and Matthew Parkin replacing Harry Middleton and Dany N'Guessan.
The second half took some time to get going, with only half chances for both sides.
Andy Little provided the first real chance of the half on the hour mark, his driving run led him to the edge of the box where he pulled the trigger, but the shot lacked the power to trouble Marosi who gathered comfortably.
It was Doncaster then with a lengthy bout of pressure, first through Jack McKay who won the ball in the box, he turned and fired at goal but it was deflected high and wide for a corner.
They were unable to make the most of the set piece but were soon on the attack again, with consecutive corners before the ball was finally cleared by Ben Roberts.
With just 15 minutes to play, the hosts made their final change of the game, with Daniel Hector replacing Billy Whitehouse.
The hosts broke again a few minutes later through a superb ball through to Jack McKay but Roberts did brilliantly to dash off his line and out of his box to clear the danger before McKay can get to it.
There were two substitutions inside three minutes for PNE that followed, with Meulensteen and Little being replaced by Dylan Davidson and Tom Barry with just ten minutes of normal time remaining.
Doncaster finished the stronger of the sides, with the breakthrough finally coming on the 90 minute mark through substitute Daniel Hector.
Hector fired at goal and produced a fantastic save from Roberts in the PNE goal, before the ball bounced in front of the line, and looked as through it was heading over the line. Clive Smith hooked it away but the referee gave the goal and the hosts progress to the next round.
PNE line-up: C.Roberts, Smith, Whelan, Jagne, B.Roberts, Heaton (c), Boyd, Adam James Robinson, Little (Barry, 80), Meulensteen (Davidson, 77), Lunney.
Unused subs: Earl, Adam Joseph Robinson, Kwateng.
Doncaster Rovers line-up: Marosi, Greasley, Carberry, P.McKay, Mbuti, Williamson, Davies, Middleton (c) (Parkin, 45), N'Guessan (J.McKay, 45), Mandeville, Whitehouse (Hector, 75)
Unused subs: Jones, Pugh.
Referee: Mr P Thompson