Mansfield have only scored once in their last six games against Northampton and the Nationwide Division Two strugglers were out of luck at the Sixfields stadium.
The Cobblers had a dream start when Paul Trollope was pulled down in the penalty area by debut goalkeeper Arjan Van Heusden in the third minute, and Marco Gabbiadini converted his seventh goal of the season from the spot-kick.
It took the home side until ten minutes before full-time to seal the points when Trollope volleyed home after Gabbiadini had headed a cross by substitute Derek Asamoah into his path.
In the meantime, the Stags bossed much of the game but were unable to turn their dominance into goals with striker Iyseden Christie showing a profligate streak in front of goal.
Christie had Mansfield's best chance four minutes after the re-start when he dashed onto a throughball from the influential Scott Sellars but he hurried his shot, firing wide of the far post.
Colin Larkin had earlier seen his glancing header drift just wide and the striker then shot tamely when given a clear sight of Lee Harper's goal.
Northampton had other chances themselves, with Chris Hargreaves directing a header against the inside of a post - the ball bouncing up into the grateful Van Heusden's hands.
Northampton boss Kevan Broadhurst, celebrating his first year in charge, was pleased with the result.
"It's all about getting the result and in four or five weeks' time, no-one will be interested how we did it," he said.
"We didn't get anything at Swindon last week when they didn't create a great deal but nobody bothered about us then."
Stags boss Stuart Watkiss tried to remain upbeat after this latest setback.
"We've probably turned in two bad performances this season and for the rest, we've been in the ascendancy," he said.
"I keep saying that things will get easier for us when the injuries start to clear up."