Substitute Shayne Bradley popped up two minutes from time to pile on the misery for the out of sorts Cobblers.
Chesterfield had lost their previous six league matches on the road but Bradley's stooping header from Chris Brandon's cross sent their fans back up the M1 in happy holiday mood.
Northampton have now lost four matches on the trot and have failed to score in that time. They deserved better than this, but were thwarted by a brilliant performance from 19-year-old goalkeeper Andy Richmond who was playing only his second senior game.
As early as the fourth minute Richmond showed his acrobatics by clipping a Jamie Forrester shot over the bar and ten minutes before the break he kept out Paul HarsleyÂ’s 30 yarder, punching it over the crossbar.
Chesterfield had chances themselves, with Rob Edwards going close in the first half with a long range drive which shaved Glyn Thompson's post while the same player should have done better late on with a close-range header that he some how managed to divert over the cross bar.
Brandon inspired the best move of the match in the 62nd minute with a fifty yard run which ended with a pass to David Reeves who's cross was inches away from being converted by Glynn Hurst.
It looked to be a stalemate until Bradley's magical moment gave Chesterfield their first league double of the season after a 4-0 win over the Cobblers in August.
Northampton manager Kevin Broadhurst said: "We are very frustrated. I thought we played quite well and were more than a match for them but fell to the sucker punch at the end.
"At the moment we're not scoring goals but I thought we defended quite well. Our local derby at Peterborough on Saturday is now a crunch game and we know we need to do a lot better." Spireites boss Dave Rushbury commented: "It is long overdue for us to get something away from home. We played with three forwards today but credit to Northampton, who kept their shape well.
"I told the players that I felt the longer the game progressed if we kept a clean sheet we could certainly go on and win it."