After falling behind to Ben Wilmot's 30-yard shot a minute into the second half, North End fought back to claim the three points.
Brad Potts volleyed them level before Andrew Hughes headed the winner in the 81st minute.
Here are the PNE player ratings with Daniel Johnson the starman - Potts and Sepp van den Berg standing out too.
1. Daniel Iversen 7
No chance with Stoke's goal. Made a good save from Alfie Doughty at 1-1, shortly before PNE's winner. Having to get used to playing out from the back a lot more. Photo: Andrew Kearns/Camerasport
2. Sepp van den Berg 8
Very assured performance in the back three, covered well down the sides when needed. The Liverpool also used the ball well from the back. Photo: Andrew Kearns/Camerasport
3. Patrick Bauer 7
The German defender played his part in limiting Stoke to just two shots on target, dealing well in the air with Steven Fletcher. Photo: Camerasport
4. Andrew Hughes 8
The defender capped a good performance with PNE's winner, a powerful header from a corner. Hughes defended well, making two important clearances from inside the six-yard box in the first half. Photo: Andrew Kearns/Camerasport