Kevin Thornton put Northampton in front on the stroke of half-time as Ian Sampson's men looked to continue the feel-good factor at Sixfields.
Two goals in four second-half minutes however won it for Chesterfield, pushing the visitors up to second in the table and leaving the Cobblers in a lowly eighteenth place.
Speaking to the official club website after the game, Sampson was left to rue the defensive errors that led to Chesterfield's goals.
"Our performance was excellent," he said.
"I don't think we deserved to lose the game."