A late header from substitute Andy Williams earned the home side the points at the County Ground.
The former Yeovil man powered a header from Ben Gladwin's deflected cross with just six minutes left to earn the win for Mark Cooper's side.
Manager Simon Grayson made just one change to the side that lost for the first time in ten games at Rochdale the previous weekend, Alan Browne coming into the midfield three, with Callum Robinson swapping places with the Irishman, taking a spot amongst the substitutes.
The Lilywhites started brightly and could have been ahead after only 90 seconds. Kilkenny picked up the ball in midfield and spread it wide to Humphrey. His cross from the right was met firmly by Joe Garner 12 yards out, but a great reflex save by Wes Foderingham denied the top scorer. The ball came back to Paul Gallagher, but the No.12 fired over the bar from left hand corner of the box.
Before the ten minute mark they had another chance to open the scoring. The whites broke quickly with Garner holding the ball up and then playing in Gallagher out wide on the left; he drove 30 yards to the edge of the box and fired across Foderingham, but the keeper made a strong save down to his left.
On the half hour mark PNE’s on loan Leicester man had another chance. He had been fouled in left hand channel 27 yards out and stepped up to take the free kick – he fired over the wall and beat Foderingham, but also beat the post, the ball flashing inches wide.
The home side were comfortable on the ball and interchanged position a lot, but were kept to scuffed shots and a couple of blocked efforts in the final minute of the half which saw Tom Clarke twice get in the way of efforts from the Robins’ midfield.
With 11 minutes of the second half gone Jamie Jones made a fine save to keep the game goalless. Michael Smith had managed to turn and earn space on the edge of the box and got a yard of space to get a shot away, but Jones made himself big and blocked well to turn the ball behind for a corner.
It was the same duo competing against each other on the hour mark as Smith capitalised on a short pass in midfield and fired low through a crowd of player, but an instinctive save by the stopper with his feet denied the home team’s top marksman.
At the mid-point in the half Kyel Reid and Josh Brownhill were introduced but it was Garner who almost made it 1-0 straight away after the changes, heading Scott Wiseman’s right wing cross towards goal, but Foderingham was well-positioned and claimed the effort.
However, with seven minutes left the visitors grabbed the lead. Ben Gladwin got some space down the right hand side and delivered a deflected ball into the edge of the six yard box to where substitute Andy Williams headed powerfully into the centre of the goal.
Kevin Davies was thrown into the action as North End had to go direct in the final five minutes with three left at the back.
Four minutes of time was signaled to be added on but the home side managed the ball and the time well and held on for the win.
Swindon Town line-up: Foderingham, N Thompson (c), Luongo, Stephens, Turnbull, Gladwin, Kasim, Smith, Toffolo, L Thompson, Obika (Williams, 71). Subs not used: Belford, Bell, Reeves, Barthram, Rodgers.
PNE line-up: Jones, Wiseman, Buchanan, Kilkenny (Brownhill, 65), Clarke, Huntington, Humphrey (Reid, 66), Welsh (c), Garner, Browne, Gallagher (K Davies, 86). Subs not used: Stuckmann, Laird, King, Robinson.
Attendance: 6,646 (319 away fans)
Referee: Mr O Langford