Nothampton Town dictated for much of the opening period and scored two excellent goals.
Tranmere were not helped by the loss of in-form Steve Davies with a leg injury after only 19 minutes, but replacement Mike Jones did well enough.
Northampton went ahead after 12 minutes. Andy Holt headed on a long clearance by keeper Mark Bunn and Andy Kirk headed home over home keeper John Achterberg.
Paul McLaren and Chris Shuker had no luck with good efforts and the Cobblers went two in front in the 39th minute.
After excellent approach work Jason Crowe crossed to the far post where Poul Hubertz headed home.
The Merseysiders should have had at least one goal just ahead of the break, but Bunn made a fine reaction save from McLaren and then did well to hold on to a close-range shot from Chris Greenacre.
It was nearly all Tranmere at the break but it was not until the 69th minute they pulled a goal back. Shuker found the target with an angled shot after the ball ricocheted off a defender.
Northampton were now at full stretch in defence, but very nearly grabbed a third goal in the 84th minute when a shot by Kirk brought a fine stop from Achterberg.
Substitute Craig Curran missed the target when set up by a faulty backpass, but Rovers levelled things out in the 88th minute with a fine header by Gareth Taylor from a deep cross by Shuker.
Tranmere almost won it in injury time but Bunn produced a terrific fingertip save to deny Shane Sherriff.
Skipper Chris Doig was excellent at the heart of Town's defence and there was a lively contribution from Holt before he was forced off through injury short of the hour.
McLaren was outstanding for Tranmere, who will feel it was two points lost rather than a point gained.