Northampton, whose away form is better than their home performances, continually frustrated the Merseysiders after taking an 11th minute lead.
It was not until the 87th minute that Tranmere pulled themselves level following a dubious penalty.
Scott McGleish was credited with the Town goal. A clearance kick by home keeper Joe Hart cannoned off him into the net in an early blow for Ronnie Moore's promotion chasers.
Tranmere went on to create some good first-half chances but Chris Greenacre fired wide from a good opening and a John Mullin header brought a diving save from Mark Bunn.
Bunn was at his best saving an angled shot by the lively Chris Shuker soon after half-time and then a Greenacre header was saved by the keeper.
Rovers made a double substitution on 63 minutes with Calvin Zola and Kevin Ellison going on. But Gareth Taylor, Zola and Paul McLaren all had no joy for the home side.
Northampton missed a big chance to double their lead when Bradley Johnson fired over when set up by substitute Ryan Gilligan in the 85th minute and the miss proved costly.
In the next minute Town defender Jason Crowe was adjudged to have handled following a cross by Shuker.
Mullin was entrusted with the spot-kick with normal penalty taker Greenacre having been substituted.
Mullin saw his shot blocked by Bunn but the rebound fell in his path and he was able to net at the second attempt.
Northampton finished strongly but Johnson had a shot deflected just wide and Luke Chambers blazed over.
Andy Holt was superb for the visitors and there was also a lively contribution from Crowe and skipper Chris Doig.
McLaren was best on the day for Tranmere but Shuker also had his moments.