Rovers always looked the better side despite the fact that Pool had most of the possession.
But the home team couldn't make it count in front of goal where they are not getting the breaks at the moment.
Hartlepool dominated a goalless first half but had nothing to show for a lot of possession and a string of wasted corners.
Tranmere's one and only chance came just before the break when substitute Theo Whitmore found himself in the clear but his attempt to lob Jim Provett posed no problem for the home keeper.
But there was a problem for Provett soon after the break when Tranmere scored the winner.
Manager Brian Little made a couple of switches after the break, changing from a 4-3-3 system to 3-5-2, and one of his substitutes scored the all-important goal on 53 minutes.
Provett saved Chris Dagnall's header with one hand, but it was Dagnall who reacted faster and he got there to prod the rebound into the gaping goal in front of Tranmere's travelling fans.
Hartlepool tried to battle back but Rovers keeper John Achterberg made some great saves.
He clutched on to a volley from Joel Porter that looked a certain goal and somehow kept out a back header from his own skipper Jason McAteer in a hectic finish to the game, during which Tony Sweeney's looping header hit the top of the bar.
But there was no way through for Pool and Tranmere dug in to solve the problems they've displayed in recent games of throwing away a hard-earned lead.