Substitute Giles Coke scored the winner five minutes after coming on in a game in which neither side really got on top of a blustery wind blowing across the pitch.
The first half was an untidy stalemate. The best chance fell to Northampton on 32 minutes when Adebayo Akinfenwa laid off a good ball for Ryan Gilligan, whose shot from outside the area on the left was tipped around the far post by home keeper Jan Budtz.
Earlier, Hartlepool's close-passing game had created a string of chances in the Northampton box, but a packed defence blocked them all before they could test keeper Mark Bunn.
First Richard Barker and Anthony Sweeney saw their efforts come straight back to them and, from the resultant corners, shots from Barker again and Michael Nelson met the same fate.
After the break, Hartlepool had the better chances as first Richie Humphreys sent his low shot inches off target and substitute Tom Craddock saw Bunn tip his shot over the bar.
But Northampton were always a threat and, the longer the home team failed to score, the more dangerous the visitors looked on the break after packing their defence for much of the game.
The winner came eight minutes from time when Coke picked up possession on the halfway line and ran at the home defence before planting a low shot into the bottom corner from the edge of the area.
Hartlepool almost found an equaliser in added time but Bunn somehow got to a low shot from Joel Porter and pushed it around the post to make sure of the three points.