Stuart Gray's men have now been beaten only once in 13 games, and while Swansea still look a good bet for the title, they have suffered a few jitters in the last week, taking only one point from a possible nine.
The game looked effectively done and dusted in the first 22 minutes when the Cobblers surged into a 3-0 lead with two goals from Poul Hubertz, one of them from the penalty spot as well as an own goal from Swansea skipper Alan Tate.
Northampton signalled their intent before scoring with Dorus de Vries spilling a fierce shot from Danny Jackman before Adebayo Akinfenwa headed against the underside of the bar from a Jackman cross.
So it was no surprise when Hubertz bagged his ninth of the season in the 14th minute when Daniel Jones' corner was headed back across goal allowing the striker to swivel and score from eight yards.
Five minutes later Jones steamed to the by-line and delivered a cross which Tate turned past his own keeper off the underside of the crossbar.
The home crowd could scarcely believe their eyes when they went 3-0 ahead almost immediately with referee Jon Moss pointing to the spot after Ferrie Bodde had brought down Ryan Gilligan, allowing Hubertz to score.
Swansea made it 3-1 in the 29th minute when Angel Zaragoza Rangel set Jason Scotland clear and the top scorer prodded home his 23rd of the season after Mark Bunn had saved his first effort.
Swansea stepped up the gas and created further chances for Guillem Bauza and Thomas Butler before the break but they should have made it 3-2 straight after the restart when Bunn dived at the feet of Scotland.
Jackman curled an exquisite fourth in the 52nd minute but Swansea never gave up the fight and Scotland netted his second of the game seven minutes from time.