The Swans had Leon Britton sent off as their three-game unbeaten run in League One came to a disappointing end at Sixfields.
A second-half goal from Luke Chambers earned the Cobblers their first home win of the season in a scrappy game where Swansea deserved something for their efforts.
Northampton Town: Bunn, Crowe, Chambers, Doig, Taylor, McGleish, Jess, Hunt, Burnell, Bojic, Quinn. Subs: Kirk, Dyche, Dunn, Watt, Gilligan.
Swansea City: Gueret, Tate, Williams, Iriekpen, Lawrence, Britton, Robinson, Tudur Jones, MacDonald, Trundle, Fallon. Subs: Austin, Akinfenwa, Jones, Oakes, Butler.
Ref: P Crossley.
Swansea went into the game without skipper Darren Pratley who picked up an injury in training on Friday.
His place in midfield alongside Owain Tudur Jones was taken by 18-year-old Shaun MacDonald.
Pratley was the only change to the side that climbed into fifth place with a win over Millwall last Sunday.
It stretched Swansea's unbeaten run in the League to three games - two of which ended with maximum points.
They faced a Northampton side in 16th place and without a win at Sixfields this season - a complete contrast to their club record run of 13 games without defeat on the road.
Despite the absence of Pratley, it was Kenny Jackett's men who started the game on top and it was only the form of Cobblers 'keeper Mark Bunn which denied Swansea taking the lead.
Bunn pulled off two great saves to deny Rory Fallon with a volley and a second shot from Andy Robinson.
The visitors didn't have it all their own way, however, as Willy Gueret was also called into action when he pulled off a brilliant save to his left to deny skipper Scott McGleish.
But while Swansea looked comfortable and played the better football, the half deteriorated into a scrappy and stop-start affair after the referee started to wave the yellow cards with Tate and Izzy Iriekpen both booked.
Half-time: Cobblers 0 Swans 0
Disaster struck for the Swans nine minutes into the second half, however, when Northampton took the lead.
A long throw from David Hunt went over the head of Tom Williams and central defender Luke Chambers unleashed a shot which flew past Gueret.
Jackett immediately made a change as Adebayo Akinfenwa replaced Fallon, but the goal still wouldn't come as Leon Britton became the third Swansea player to be booked.
Britton moved into the middle with 15 minutes to go as 17-year-old Chris Jones came on for MacDonald. It nearly had the desired effect as Britton turned his marker only to be denied by Bunn.
Swansea had their best spell off the half in the final 10 minutes, but their hopes looked to have evaporated when Britton was sent off at the end of normal time for a second yellow card.
Despite five minutes of added time, Swansea couldn't make the breakthrough.
