Ronnie Moore made a number of changes to the side that drew 1-1 with Yeovil, as Tremarco, Kay, Achterberg and Ahmed replaced Sherriff, Goodison, Coyne and McLaren. Whilst Goodison, Coyne and Sherriff were on the bench, they were joined by Mike Jones and academy player Terry Gornell.
Tranmere started poorly as Morecambe, who have already knocked Wolves and Preston out of the League Cup this season, had the first shot of the game, Achterberg pushing the ball round the post from Blinkhorn's powerful drive before Tranmere had their first shot of the game on 19-minutes, Davies heading over from Ahmed's cross.
A 25-yard Hunter drive was straight at Achterberg nine minutes later before Davies again headed wide, this time from Shuker's cross, soon after.
Chances were few and far between and it wasn't until the 43rd minute that Tranmere had their next chance, Davies again in the action as he shot over from near the touchline.
With not long to go in the half, Morecambe had the best chance of the game so far as John Achterberg made one of the saves of the season so far, tipping over Hunter's rising shot with some spectacular acrobatics.
After what the Rovers fans hoped would be an inspirational half-time team talk from Ronnie Moore, Mike Jones replaced Chris Shuker on the right-wing and almost straight after the re-start Greenacre shot narrowly over from Davies' knock down.
Davies show just wide himself from 16-yards on 52-minutes after good build up play involving Greenacre and Jennings before Morecambe took a surprise lead on 55-minutes.
After a quick counter-attack, substitute Lloyd found Hunter inside the area and the Morecambe player let go an unstopable shot which flew into the top corner from about 14-yards from goal, leaving John Achterberg with no chance.
It was all up hill for Rovers now as they pushed for the win. Jennings shot over from distance before Curran again missed the target after Blinkhorn had dragged a shot wide for Morecambe.
Ahmed was then almost in from Davies' accurate cross but the ball was put out for a corner before it reached the former Manchester United man and from the resulting set-piece Kay headed over.
After mistakes from both Stockdale and Chorley at the back, with the right-back Stockdale in particular going missing for the goal, Ronnie Moore replaced Stockdale with Ian Goodison as Anthony Kay moved to right-back.
Kay again missed the target but in more unlucky circumstances after the substitution, the defender cutting in from the right and bending a left-footed shot just wide of the target.
An Ahmed lob drifted just wide soon after and Steve Davies was unlucky not to score as a number of his long range efforts were blocked by the Morecambe defence.
In the end, it wasn't Rovers' day and a trip to Wembley, unless Rovers make the play-off finals, looks unlikely for another season.
Jones' Man Of The Match: Rovers were poor all round with no real stand out performances. However, Anthony Kay did stand strong and look good in his performance at both centre-back and right-back, as he played a number of great cross-field balls and defended well.