Match report: Huddersfield 3 PNE 2
Referee Lee Probert pointed to the spot in the 94th for an off-the-ball clash between Jordan Hugill and Elias Kachunga.
After a delay due to PNE's protests, Aaron Mooy's penalty was parried by Chris Maxwell but substitute Collin Quaner followed-up to fire home the rebound.
It was harsh on the visitors who had looked to have earned themselves a point in West Yorkshire.
Aiden McGeady had fired them ahead with a superb shot from 20 yards in the first half, only for Kachunga to head Town level two minutes before half-time.
Jack Payne headed a fortuitous goal in the 71st minute to give Huddersfield the lead.
But Hugill levelled eight minutes later, heading home a cross from Tom Barkhuizen.
Then came the late controversy, PNE manager Simon Grayson protesting to Mr Probert as he left the pitch at the final whistle.
Gone are North End's play-off hopes with four games to play, although the point which was denied them would not have made much difference - only a victory would have kept their faint hopes alive.
Grayson had made two changes to the starting XI, Jordan Hugill returning after missing the Leeds game with concussion and Daniel Johnson drafted back into midfield.
Alex Baptiste was missing through suspension, while Callum Robinson dropped down to the bench.
North End started 4-4-2, DJ on the left wide of midfield, McGeady on the right with Ben Pearson and Paul Gallagher in the middle.
Huddersfield made the early running, a cross from Chris Lowe travelling through to Kachunga who's shot struck Paul Huntington's out-stretched leg and forced Maxwell to dive to his right to parry.
Greg Cunningham got in a great clearing header as the home side pressed in the next attack.
A low shot from Rajiv Van La Parra, struck from the edge of the box, was saved comfortably by Maxwell.
North End lost Tom Clarke to injury in the 17th minute, the skipper feared to have torn the Achilles tendon in his right leg
After briefly being treated on the pitch, he was helped off by physio Matt Jackson, handing the armband to Gallagher.
Tommy Spurr replaced him from the bench, Spurr going to left-back with Cunningham moving across to partner Huntington in the centre of defence.
PNE's 24th minute opener came out of nowhere, Gallagher's pass from midfield finding McGeady down the right channel.
McGeady pushed forward, went past a defender before driving a right-foot shot from 20 yards into the top corner over goalkeeper Danny Ward.
For a time, the visitors looked comfortable with their lead, pressing Huddersfield high to try and prevent them playing out from the back.
Huddersfield levelled two minutes before the interval, Aaron Mooy's corner from the left missed by Maxwell was he came to collect, the ball travelling to an unmarked Kachunga who headed home at the back post.
Nine minutes into the second half, Kachunga got played away down the right hand side of the box but from a tight angle fired into the side-netting.
Ben Pearson collected his 15th yellow card of the campaign in the 58th minute, the midfielder clashing with Lowe after Tom Barkhuizen had been fouled.
He now faces a three-match suspension and a likely appearance before the FA.
Marnick Vermijl and Huntington were also booked soon after as the game hit a scrappy spell and tempers got a bit heated.
Vermijl got round well on the cover to prevent a ball over the top reaching Nahki Wells.
Huddersfield took the lead when Wells' ball out to the right hand side of the box found Tommy Smith.
The home skipper totally miscued his volley but the ball bounced across goal to substitute Payne who sent a diving header into the net.
Back came North End and in the 79th minute, Johnson got the ball in the box and finding his path blocked, slipped a pass back to Barkhuizen on the side of the penalty area.
Barkhuizen lifted a cross into the middle for Hugill to power a header into the roof of the net from eight yards.
It looked enough to earn a draw until the stoppage-time drama of Huddersfield's penalty.
There was plenty of confusion as Mr Probert halted play without appearing to point to the spot, only doing so as players from both sides surrounded him.
Replays showed Hugill and Kachunga together just inside the box, but there was no sign of the stamp and push which the referee later told Grayson he had seen.
Maxwell was booked for time-wasting with it two minutes from play stopping to the penalty being taken.
Mooy hit the spot-kick right-footed, Maxwell diving to his left and pushing it away.
But it fell to Quarner on the corner of the six-yard box, the German driving a first-time shot into the net.
Huddersfield: Ward, Smith, Schindler, Hefele, Lowe, Hogg, Billing (Payne 36, Hudson 90), Kachunga, Mooy, Van La Parra, Wells (Quaner 86). Subs (not used): Whitehead, Scannell, Cranie, Coleman.
PNE: Maxwell, Vermijl (Browne 88), Clarke (Spurr 17), Huntington, Cunningham, McGeady Pearson, Gallagher (Horgan 74), Johnson, Barkhuizen, Hugill. Subs (not used): Makienok, Beckford, Robinson, Lindegaard.
Referee: Lee Probert (Wiltshire)
Attendance: 21,254 (1,663 PNE)