Peter Hartley's first half header was enough for Hartlepool as Rovers were defeated 1-0 at Victoria Park.
It was a hard loss for Rovers who created plenty of chances throughout the 90 minutes with Gareth Edds,Terry Gornell and John Welsh all going close.
Caretaker Manager Les Parry named an unchanged team as Paul McLaren recovered from a knock on his hip to take his place in the centre of midfield alongside Gareth Edds and John Welsh. Luke Daniels returned from suspension to take a place on the substitutes' bench.
Terry Gornell had the game's first chance with the striker meeting a Paul McLaren corner at the near post only for his header to be saved by Scott Flinders. Seconds later Edds headed goalwards but his effort was also cleared off the goal line.
At the other end Adam Boyd tried an overhead kick from the edge of the area but the former Luton Town striker put his shot well wide of the target.
Ian Thomas-Moore saw a shot saved by Flinders on seven minutes while David Martin watched as a Hartlepool effort went just over his bar soon after.
A couple of long range efforts from Thomas-Moore failed to hit the target while strong wind and rain didn't help either side during a period that saw both give away possession from promising positions.
Midfielder John Welsh sent a volley just over the bar from 20 yards on 34 minutes and Marlon Broomes blocked a Boyd effort soon after. However, the home side took the lead a couple of minutes before half time. A ball across the area from Ritchie Jones deflected off the head of McLaren to Peter Hartley at the far post and he made no mistake in heading in from close range.
Ian Goodison failed to connect with a Welsh cross on 47 minutes and Craig Curran curled a shot wide a minute later as Rovers began the second half well.
Hartley shot wide when trying to double his side's lead and Rovers had to deal with a couple of corners in quick succession soon after.
Flinders had to turn a Curran cross over the bar on 71 minutes and Chris Shuker and Charlie Barnett were introduced to the action to give Rovers fresh legs. Shuker shot across the face of goal soon after joining the action, while Edds fired at Flinders moments after Kithson Bain had replaced Curran.
At the other end Martin held Richie Humphreys' long range effort and the keeper dealt with a Behan shot after good work from Goodison.
Rovers' task was made harder when Barnett was shown a straight red card by referee Gary Sutton and though chances came in injury time, they were unable to beat the Hartlepool defence.
Hartlepool: Flinders, Austin, Collins, Liddle, Hartley, Brown (McSweeney 78), Jones, Humphreys, Monkhouse, Boyd (Greulich 72), Behan. Substitutes not used: Cook, Haslam, Sweeney, Fredriksen, Bjornsson.
Tranmere: Martin, Logan, Broomes, Goodison, Bakayogo, Edds, Welsh (Barnett 75), McLaren, Curran (Bain 81), Thomas-Moore, Gornell (Shuker 67). Substitutes not used: Daniels, Taylor, Cresswell, Mahon.
Referee: Gary Sutton
Yellow cards: Behan (62), Welsh (63)
Red card: Barnett (89)