The first half score few chances for either side with the game looking like it would end it a 0-0 bore draw.
All of Swindon players were playing below their best, as they failed to take advantage of some poor Northampton defending.
Northampton's goal came on 61 minutes after Bart Griemink who before then had little to do all game made a great save to push the ball over the bar and away for a corner, but Harsley scored from the corner.
Sam Parkin did come close to scoring when the Northampton keeper kicked the ball out only for it to hit Parkin and come back, but Northampton were able to clear the ball away just in time.
In the last few minutes if the game Andy King and the Northampton assistant manager were both sent off from the bench after clashing with each other in what was the high light of the game.
Swindon also had a last minute penalty decision for hand ball turned down.
Overall a poor game in which Swindon never looked like scoring, Swindon now face Cheltenham at home on Wednesday night after the game was called off last Wednesday due to a waterlogged pitch.