It gave the home side only their second win in ten matches and sets them up nicely for Tuesday night's dog fight with Swindon.
Adebayo Akinfenwa returned from a month long suspension and fired the hosts in front after 12 minutes when he converted a cross ball from Aleksander Prijovic who was making his debut after signing on loan from Derby in the week.
The Cobblers made it 2-0 in first half stoppage time when a corner from man of the match Luke Guttridge eluded everyone and fell to Abdul Osman who slid the ball home at the back post.
The hosts wrapped up the points with 19 minutes to go when Guttridge seized on a loose ball on the right edge of the penalty area and rammed a low shot past Owain Fon Williams.
There was still time for Northampton's second debutant of the afternoon to make his mark. Scott Vernon was signed on loan from Colchester in the week and came on as a 64th minute replacement for Akinfenwa. His golden moment arrived when Fon Williams failed to hold a deep cross from Liam Davis after a surging run down the left and the striker simply had to tap home the loose ball.
Chris O'Grady worked hard as a lone attacker for the visitors, although he could have done better with County's best chance of the first half in the 20th minute when he blazed wide. The visitors had a goal disallowed when Leon McSweeney's effort was ruled out by a linesman's flag after O'Grady had forced the initial save from home goalkeeper Chris Dunn.
O'Grady kept trying to the end and saw a last minute drive flash inches wide but County's season is in danger of falling apart after a run of only one win in seven matches which has virtually extinguished their play-off hopes.