The defeat follows Tranmere's run to the final last season, when they were squedualled to play Marine but thefxiture could not be fullfilled and so the competition was not completed.
Rovers, lining up with first teamers Steve Davies and Craig Curran in their side along with Paul Henry, Mike Johnston and Danny Holmes, were under pressure from the off as they struggled to cope with the pace of Everton striker Agurd.
Everton took the lead on 19 minutes after Kissock's shot was deflected wide for a corner. From the resulting set-piece, Morrison beat Johnston to a near post header, as he flicked the ball past McWeeney into the net.
Less than a minute later, Kevin Sheedy (the former Tranmere assistant and caretaker manager) wathced his side double their lead after a brilliant counter attack.
Kissock broke down the Tranmere right and passed the ball through Danny Holmes' legs in field to Morrison, who scored his second of the game as he slotted past McWeeney for the second time.
McWeeney saved from the troublesome Agurd on 26-minutes whilst Gornell forced Jamie Jones in the Everton goal into making a save soon after as Tranmere looked to get back in the game.
The second half saw Tranmere come out fighting and they were the better team for much of the 45-minutes.
On 56-minutes they got back into the game thanks to a deflected strike from Olly James, moved from midfield after the departure of injured captain Paul Henry.
Everton failed to clear a cross from right-back Luke Denson, with the ball falling to James 25-yards from goal. The 19-year old took the ball down on his chest before shooting towards goal. Jamie Jones was left wrong footed in the Everton goal after the ball took a cruel deflection.
Tranmere now looked for a winner but they simply couldn't find the back of the net, despite having numerous chances to level the game.
Craig Curran headed narrowly over from a Luke Denson cross before Steve Davies also saw a header miss the target.
With just minutes left on the clock, Tranmere had their best chance of the game as striker Terry Gornell brought the ball down just outside the six yard box before hitting a powerful effort towards goal. However, his shot was blocked and the game stayed at 2-1.
Everton then went on to win the trophy although the result could have been so much different if Rovers midfielder and captain Paul Henry had not limped off with an ankle injury in the 10th minute.
The man of the match for Rovers was goal scorer Olly James. Starting the game at right-back, James was moved to central midfield (he can also play upfront!) when young Luke Denson replaced Paul Henry after ten minutes. He adapted well to the new position however, putting in a number of good tackles and spreading the ball well to wingers Holden and Davies.
Look out for more reserve new coming on the site next season.