Northampton were denied the win by Darlington goalkeeper Sam Russell.
Russell kept his side in the game with a string of saves to extend the visitors' unbeaten run to five matches.
Darlington took a 23rd minute lead after Ryan Valentine's cross was flicked on by Alun Armstrong to Craig Hignett, who drilled the ball home.
Town striker Steve Morison was denied by a superb Russell save before the break, but he made no mistake on 52 minutes after Josh Low had crossed.
Darlington: Sam Russell, Fleming, Liddle, Clarke, Kendrick (Wainwright 56), Valentine, Close, Keltie, Clark, Armstrong, Hignett (Convery 27), Convery (Gregorio 81).
Subs Not Used: Maddison, Hughes.
Goals: Hignett 23.
Northampton: Rachubka, Low, Willmott, Murray, Bojic, Cozic, Galbraith (Jaszczun 75), Williamson (Amoo 88), Youngs, Morison, Sabin.
Subs Not Used: Bunn, Chambers, Hicks.
Goals: Morison 53.
Ref: M Pike (Cumbria).