Northampton clambered off the foot of the Division Two table thanks to a goal in each half from Derek Asamoah and Ian Sampson.
For County, this was their first defeat in seven matches but they could have few complaints as the Cobblers greater urgency won the day.
Asamoah latched on to a probing through ball from Greg Lincoln in the 24th minute before firing sharply past Steve Mildenhall in the visitor's goal, while Sampson, who had an effort ruled at Cheltenham on Saturday, made no mistake with a thundering header from Paul Harsley's corner eight minutes from time.
Northampton's assistant manager, Mark Kearney, standing in for absent boss Martin Wilkinson, said: "We have given ourselves a chance with this victory. There is still a lot of football to be played but if we concentrate on the performances then the results will come." He added: "Notts County enjoyed some possession but didn't hurt us in any way.
"We stopped them getting the ball into Heffernan and Stallard up front. I thought Sampson and Paul Reid were outstanding in the middle of our defence." Loan striker Lawrie Dudfield was making his home debut and could have clinched the points earlier for the hosts but he shot tamely from close range four minutes after the restart.
That meant the jitters continued for longer, but County's best efforts were restricted to shots from distance, with Richard Liburd and Paul Heffernan both testing Lee Harper from outside the box.
And five minutes from time Darren Caskey floated a free-kick over the crossbar and with it disappeared the Magpies final chance of prising anything from this contest.
County boss Billy Dearden said: "We still have a bit of work to do this season.
"People thought we were going to come to Northampton and win the game but I knew it would be tough as they are fighting for their lives.
"You have to do more than we managed tonight to win a football match."