Luckless Stockport remain in the Nationwide Division Two relegation zone after this latest defeat which hinged on two disputed penalties and an own goal.
Twice the visitors fought back to draw level. They were much the better side on the night but fell to defeat due to a second spot-kick three minutes from time.
Ryan Taylor was the Tranmere hero. He converted both penalties and also created the other goal with his corner kick that took a deflection off Hatters skipper Jim Goodwin.
Goodwin conceded the first penalty in the fifth minute for a push on Eugene Dadi. Taylor netted into the top left corner.
County rallied but Fraser McLachlan headed wide from a simple chance and then Ali Gibb fired over.
John Achterberg made a fine save from Rickie Lambert in the 31st minute before the equaliser finally came in the 34th minute through Danny Griffin with a shot from just inside the box after a partly-cleared corner.
Simon Lynch hit a post for the visitors in the 58th minute before Tranmere regained the lead six minutes later from Taylor's corner.
It was 2-2 on 73 minutes with McLachlan heading Danny Jackman's cross home after an excellent four-man move.
But in the 87th minute County's loan keeper Anthony Williams, on his debut, was pulled up for a push on Gary Jones and Taylor this time put the spot kick into the top right-hand corner.