Aidy Boothroyd's side once again were left with a mountain to climb away from home by being reduced to ten men as Ishmel Demontagnac received a first-half red card.
The Cobblers held out until the 53rd minute but a quickfire brace for the home side from Bamford and Ali secured their passage into the next round of the Johnstone's Paint Trophy.
Boothroyd did not defend Demontagnac after the game and was left frustrated that a dismissal once again hampered his side.
"I couldn’t ask for any more from my players and 99 per cent of the fans could see they had a go."