Martin Foyle's men had slipped to within touching distance of the relegation zone but bagged three precious points courtesy of Danny Whitaker's second-half strike at Vale Park.
The home side almost bagged themselves an early goal when Leon Constantine's clever flick inside the box set up Akpo Sodje for a headed chance but the striker dispatched the ball poorly over the bar.
The 20th minute saw both sides come alive briefly with the Cobblers coming close after Mark Hughes' cross was redirected by the head of Kenny Deuchar only for Joe Anyon to collect.
The Valiants broke quickly through Malvin Kamara and, after dashing down the right flank, the former Cardiff man supplied a pinpoint cross only for Sodje to squander once more.
Sodje made it a hat-trick of misses seven minutes later when, after Danny Sonner's failed free-kick was lofted back into the box, the targetman somehow failed to find the back of the net.
Chances weren't hard to come by in the first half as Northampton once more sprung Vale's offside trap with Deuchar eventually getting a sight of goal from 12 yards that was superbly blocked by Anyon.
Foyle's half-time team-talk must have hit home as Vale took the lead two minutes after the restart when a poor clearance laid the ball at Whitaker's feet for him to bury past Mark Bunn.
Northampton should have drawn level in the 50th minute when Deuchar's header looked to be heading for the goalkeeper's bottom left corner only for Anyon to fly into action and tip the ball around the post.
Sodje seemed determined to get his name on the scoresheet and came as close as was going to come in the 61st minute.
After a clever flick on from fellow forward Constantine, he unleashed an unstoppable left footed strike from the edge of the box that cannoned back off the underside of Bunn's crossbar.
Northampton boss Stuart Gray tried to freshen up his flagging side with the addition of David Hunt and Jordan Robertson but it had little effect as Port Vale held on to claim a morale boosting victory.