Kevin Thornton levelled for the visitors just before half-time but Ian Sampson's men were undone by a quickfire double from Jake Robinson after the break.
Not the result Sampson would have wanted although he will have little trouble picking his men up for their next game, which is away at Anfield in the League Cup next week.
The Cobblers boss however was keen to stress to the official club website afterwards that his priority is next weekend's trip to Bradford City and also signing a new centre-back on loan.
"I've made a few phone calls to do that but they have been knocked back but we will keep trying."