Craig Curran got the game's only goal as hard-working Tranmere posted their first success of the season, ending Hartlepool's 100% start.
The striker netted with a fine strike after Edrissa Sonko flicked on a long Ben Chorley clearance on 23 minutes.
Another Curran effort was ruled out for offside just short of the hour, but Hartlepool also had their chances.
A Gary Liddle effort was somehow hacked clear by Chorley and the same player was later denied by keeper Danny Coyne.
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Ronnie Moore told BBC Radio Merseyside: "I think overall we've had enough of the game and deserved to win it.
"We've had a little bit of good fortune around our box but I think it's been good defending rather than their attacking ideas."
Tranmere: Coyne, Antwi , Chorley, Goodison, Taylor, O'Callaghan (Savage 71), Jennings, Kay, Moore (Edds 86), Curran, Sonko. Subs Not Used: Achterberg, Greenacre, Shuker.
Goals: Curran 23.
Hartlepool: Lee-Barrett, Sweeney, Nelson, Collins, Humphreys, Jones (Foley 59), Boland (McCunnie 83), Liddle, Monkhouse (Barker 77), Porter, Brown. Subs Not Used: Power, Robson.
Att: 5,418
Ref: Jon Moss (W Yorkshire).
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