John Gorman's side have been brilliant on the road, but they can't get it right in front of their own fans.
Vale's early season hot streak had dipped in recent weeks, but they bounced back to earn just their second win in eight matches thanks to a headed goal from skipper George Pilkington and a deflected drive by Stefan Moore.
Pilkington opened the scoring in the 12th minute when he met a far post corner from Danny Whitaker to power his header into the net.
At the other end, Mark Goodlad twice saved within seconds from Andy Kirk in the 20th minute, while on the home side Mitchell Cole was proving a menace down the left wing.
But it was the visitors who stretched their advantage in the 32nd minute when a long throw into the box by Richie Humphreys was only half-cleared and Moore struck a low shot which was deflected past Mark Bunn.
Bunn then made an excellent save to parry away a long-range effort from Vale's top-scorer Leon Constantine who then fired a free-kick over the bar before the break.
Northampton stepped up the pressure after half-time with substitute Jerome Watt seeing his shot beaten away by Goodlad before going close three minutes later with a left-foot drive which flew just wide.
Vale were content to soak up the pressure and Northampton's David Hunt almost capped an excellent game with a goal when he sent a 25-yard free-kick screaming wide with just 20 minutes left.
Vale substitute Nathan Lowndes forced Bunn into a diving save with seven minutes left, but it was the home side who finished on top when Northampton's leading scorer Scott McGleish saw an 86th minute header from Watt's cross come back off the post.