A first half goal from Jose Baxter wasn't enough for Rovers as they lost 2-1 at home to Sheffield Wednesday.
Tranmere had the better of the first 45 minutes but a late equaliser from Chris Lines saw the sides go into half time all square.
The visitors dominated the early stages of the second half and though Rovers came back into the game, Ryan Lowe's header ten minutes from time gave the Owls the win.
There was one change to from the team that started against Cheltenham in the FA Cup as Jose Baxter returned from suspension to take the place of Adam McGurk, with Andy Robinson moving to left wing. Enoch Showunmi missed out through injury while Martin Devaney and Mark McChrystal were named on the substitutes' bench.
After a high paced opening to the game Rovers almost took the lead on seven minutes. Reda Johnson's miss hit clearance went straight to Jose Baxter 30 yard out in a central position and spotting the goalkeeper off his line the Everton loanee sent an attempted lob just inches over the bar and onto the roof of the net.
A looped pass down the right wing from Dave Raven found John Welsh on 21 minutes and the midfielder did well to find Mustafa Tiryaki with his first time cross but the striker put his header over the bar.
A Baxter shot appeared to strike the arm of a Wednesday defender on the edge of the area on 22 minutes but play continued and Rovers stayed deep in the visitors' half, winning a couple of corners in quick succession.
Tranmere had the ball in the Wednesday net on 29 minutes but Taylor's effort was ruled out for offside. The defender headed in from close range after David Buchanan's pass into the area had been knocked into the path of Baxter by Ian Goodison, and the ball was quickly whipped into the six yard box.
Wednesday's first shot of the game came on 36 minutes with Chris Lines shooting straight at Owain Fon Williams from 25 yards after good hold up play from Chris O'Grady inside the area.
Rovers were quickly back on the attack and after Baxter had fired over from long range on 37 minutes, the 19-year old found the net two minutes later. A long ball forward into the Wednesday area was only cleared as far as Baxter 25 yards out. He shaped for a first time volley but instead turned inside his defender, found space in front of him and his right foot shot took a deflection and beat Stephen Bywater at his left hand post.
However, just as the board went up to indicate three minutes of added time at the end of the half, the visitors levelled. A long throw in towards the Tranmere near post was turned away from the six yard box but only as far Chris Lines on the edge of the area whose low shot went through a crowded box and crept past Fon Williams into the right side of the goal.
Bywater dropped a Robinson cross in the first minute of the second half but he was quick to react and gather at the second attempt.
Lines curled over the top right corner for Wednesday on 50 minutes and Fon Williams had to catch on his goal line from Johnson as the visitors pressed from a corner soon after.
Buoyed by the goal on the stroke of half time, Wednesday started the second half the brighter of the two sides and saw Liam Palmer fire just wide of the right hand post from 25 yards before O'Grady hooked a shot past the target on 54 minutes.
A slip from Palmer gave possession to Robinson on 67 minutes and he wasted no time in taking on a defender and firing in a low shot which was parried by Bywater.
Tiryaki was replaced by McGurk on 68 minutes with Akins moving into the central striker's role. Akins quickly got involved in his new position, rolling the ball into Baxter's path with his strike partner shooting across Bywater and just inches past the far post.
Lowe won possession off Goodison on 71 minutes and found O'Grady who sent a first time effort over the bar while Lowe's near post effort had to be turned around the post by Fon Williams eight minutes later.
However, Lowe headed his side into the lead from the resulting corner, nodding in at the far post following a scramble.
Rovers responded by introducing Martin Devaney in place of Robinson and after Baxter volleyed over from Weir's lay off, Weir was replaced by Labadie in midfield.
Devaney headed straight at Bywater after Fon Williams' long clearance was played into his path by Wednesday defender Jones while substitute Julian Bennett fired over at the other end soon after.
Two late corners for Rovers even saw Fon Williams in the opposition area but the closest they came to an equaliser was a powerful 18-yeard effort from Labadie that went wide of the target.
Tranmere: Fon Williams, Raven, Taylor, Goodison, Buchanan, Akins, Weir (Labadie 85), Welsh, Robinson (Devaney 82), Baxter, Tiryaki (McGurk 68). Unused substitutes: Coughlin, McChrystal.
Sheff Wed: Bywater, Johnson, Lines, Batth, O'Connor, Palmer, Madine (Lowe 45 HT), Semedo, O'Grady, Marshall (Bennett 87), Jones. Unused substitutes: O'Donnell, Prutton, Morrison.
Referee: Roger East
Yellow cards: Welsh (17), Weir (58), Jones (72)
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