Adebayo Akinfenwa scored his seventh goal of the season as the Cobblers overcame Crewe to record only their second league win of the season.
Danny Jackman expertly curled a free-kick over the wall for the opener but the hosts soon drew level when Tom Pope flicked in Billy Jones' cross.
Akinfenwa drilled in the 63rd-minute spot-kick with ease after Mark Little had been brought down by Jones.
And Abdul Osman sealed the points when he rose to head home Jackman's corner.
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Crewe first team coach Steve Holland told BBC Radio Stoke:"Defensively we were fine but we didn't cause them any problems." "All our defenders are told that if you go to ground in the area then you run the risk. Officials are only human and they give what they see."
"I was disappointed with both our wingers. Joel Grant didn't get into good positions and when he had the ball he didn't use it like he can."
Crewe: Collis, Woodards, O'Donnell, Lawrence, Jones, Moore (Miller 68), Bailey (Grant 19), O'Connor, Carrington, Elding (Zola 68), Pope. Subs Not Used: Schumacher, Brayford.
Booked: O'Connor.
Goals: Pope 55.
Northampton: Fielding, Little, Hughes, Crowe, Davis, Guttridge, Osman, Jackman, Holt, Akinfenwa (Constantine 72), Hawley (Gilligan 83). Subs Not Used: Dunn, Doig, Coke.
Booked: Davis, Crowe.
Goals: Jackman 45, Akinfenwa 64 pen, Osman 70.
Att: 3,977
Ref: Andy Haines (Tyne & Wear).
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