Ben Clark's late penalty eased Hartlepool's relegation fears in a game that was marred by a strong wind.
Both sides struggled to create many chances, but Pools took the lead midway through the second-half when Michael Nelson drove a shot in from 18 yards.
One minute later Tranmere's Ben Chorley looped a header over Arran Lee-Barrett from Andy Taylor's free-kick to level.
However, Antony Kay brought down Lewis Guy in the penalty area and Clark tucked in the winner from the spot.
Hartlepool: Lee-Barrett, Sweeney, Nelson, Collins, Humphreys, Jones (Henderson 90), Clark, Liddle, Monkhouse, Guy (Mackay 85), Parker. Subs Not Used: Foley, Rowell, Cook.
Goals: Nelson 69, Clark 83 pen.
Tranmere: Achterberg, Edds, Chorley, Kay, Taylor, Sonko, Jennings, Henry (Gornell 84), Barnett, Moore, Shuker. Subs Not Used: Coyne, Cresswell, Waterfall, Macauley.
Goals: Chorley 70.
Att: 3,033
Ref: Carl Boyeson (E Yorkshire).
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