The players struggled to get to grips with a fierce wind that blew rain down the pitch and the elements proved to be of little or no advantage for the home team, who had it at their backs from the start.
The best either team could muster early on was a curling 25-yard shot from the left by Hartlepool's Andy Monkhouse but, after swerving in the wind, it went well wide of the far post.
Otherwise, it was a tale of Hartlepool over-hitting the ball as the wind pushed them forward and Tranmere at times struggling to get the ball out of their own half.
Five minutes before half-time, Hartlepool left-back Richie Humphreys sent on a 30-yard shot that looked dangerous until it was blocked deep in the Tranmere area.
The rain eased after half-time but the wind didn't and life was just as difficult for both teams as it had been earlier.
A long clearance from keeper John Achterberg gave Tranmere an early chance as Ian Moore closed down home keeper Arran Lee-Barrett, who grabbed possession at the second attempt after Antony Sweeney cleared the bouncing ball off his own line.
Hartlepool took the lead on 69 minutes as the game at last came to life.
Defender Michael Nelson blasted home an unstoppable shot from the edge of the area after Richie Jones did well on the right before squaring the ball inside.
But within a minute, Tranmere were level when Ben Chorley got on the end of a free-kick by Andy Taylor and looped his header over Lee-Barrett and into the net.
But Hartlepool won it nine minutes from time when Paul Henry was judged to have fouled Lewis Guy in the area and as the protests died down, Ben Clark scored from the spot to earn three points.