Trailing to a Freddie Sears goal in the Johnstone's Paint Trophy at Sixfields, the Cobblers fought back with strikes from Bayo Akinfenwa and Henoc Mukendi to make it into the next round.
The visitors from League One were reduced to ten men in the dying stages of the game as they fought in vain to take it to a penalty shoot-out and their performance after half-time left manager Joe Dunne 'furious'.
“We could have been three or four up in the first half easily and we dominated the game," he said.
“We said to them at half-time that they’ll come out and do what they do in the first ten minutes but we didn’t stand up to it."
Having seen his old club defeated, Aidy Boothroyd will now look for his side to end their mini-slump in League Two at the weekend when Exeter City are the visitors.