Derek Adams’ players face either Newport County AFC or Forest Green Rovers at Wembley after Sunday’s draw gave them a 3-2 aggregate win.
Leading 2-1 from the first leg, Morecambe extended their overall advantage through Aaron Wildig’s early goal.
James Vaughan gave Tranmere hope when he levelled matters on the day seven minutes into the second half but the Shrimps, aided by keeper Kyle Letheren saw out the remainder of the game.
Adams was forced into one change from the side which won Thursday’s first leg.
Stephen Hendrie’s ankle ligament injury saw him replaced by Liam Gibson with Kelvin Mellor, back from suspension, on the bench.
With fans inside the Mazuma Stadium for the first time this season, Adams’ players started briskly - almost as if they were keen to give them something to cheer about early on.
It almost happened on six minutes when Liam McAlinden got behind the Tranmere defence but keeper Joe Murphy was out quickly to block.
Then, if it were needed, the fine lines evident in League Two all season were displayed within the space of 60 seconds.
McAlinden was dispossessed deep in the Morecambe half, Tranmere working the ball to Liam Ridehalgh.
He drove a cross into the Morecambe area and Vaughan’s diving header hit the top of Letheren’s crossbar.
The Rovers striker was angry a corner wasn’t awarded and, seconds later, the Shrimps were in front.
McAlinden threaded the ball through for the onrushing Wildig to take a touch and slot home his 10th of the season.
They came close to a second on the quarter-hour, firstly when Peter Clarke’s last-ditch clearance thwarted Yann Songo’o.
From the resulting corner, Sam Lavelle’s header was turned away by Murphy as the Shrimps had much the better of the early stages.
In contrast, the visitors largely continued from where they left off in the first leg, enjoying some decent possession but struggling to break through a resolute Morecambe defence.
Corey Blackett-Taylor, so impressive in the first half of Thursday’s first leg, saw a shot blocked, while Vaughan’s rising drive comfortably cleared the crossbar.
However, with Songo’o, Gibson and Toumani Diagouraga especially impressive in their defensive efforts, Morecambe were relatively untroubled.
That was until the last minute of the first half when the Shrimps failed to clear a cross and Letheren made an excellent low save to keep out Paul Lewis’ volley.
Tranmere made two changes at the break, introducing David Nugent and Otis Khan and changing formation in an attempt to find a greater cutting edge in attack.
It paid off within seven minutes of the restart when they pulled level on the day.
After Letheren had been forced to tip one corner over the bar, the subsequent set-piece was struck at goal by Nugent and Vaughan netted from close range.
It left Morecambe needing to negotiate a difficult passage of play in which the visitors began to sense an equaliser.
As in the first leg, it was helped by Morecambe struggling to retain possession when it was played up to Stockton though, in fairness, he was afforded little protection from the officials.
Back came the Shrimps, however, with Diagouraga having a shot deflected over before Jay Spearing’s intervention denied McAlinden on the counter-attack.
However, it was Letheren who preserved their aggregate lead 10 minutes from time, making a fine save from Manny Monthe’s header.
Tranmere moved Clarke from centre-half to centre-forward as they threw the kitchen sink at the Shrimps, assisted by six minutes of added time.
Their final ball lacked the necessary quality, however, and Morecambe were able to play out time and secure their place in the final.
Morecambe: Letheren, Cooney, Knight-Percival, Lavelle, Gibson, Songo’o, McAlinden (Lyons 82), Diagouraga, Wildig (Kenyon 88), Mendes Gomes, Stockton. Subs not used: Halstead, Mellor, Davis, Leitch-Smith, Pringle.
Tranmere Rovers: Murphy, O’Connor (Khan 46), Clarke, Monthe, Ridehalgh (Macdonald 64), Spearing, Lewis, Morris (Nugent 46), Feeney, Vaughan, Blackett-Taylor (Woolery 64). Subs not used: Jones, Nelson, Crawford.
Referee: Thomas Bramall.
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