Having knocked out three League 1 sides in earlier rounds Jim Bentleys side couldn’t repeat the feat as goals from David Ball and Jimmy Ryan settled this Northern Area semi-final tie.
In difficult conditions the hosts started on the front foot, Bobby Grant twice seeing left-footed shots from 20 yards go narrowly wide in the opening 10 minutes.
Morecambe settled but were largely playing on the back foot, one poor kick from Tony Thompson, on his first Shrimps start, gifting the lively Tariqe Fosu a run on goal that ultimately came to nothing.
Everton loanee David Henen was the next to go close for the hosts but the Belgians low, curling shot was beaten away by Thompson.
It was increasingly one way traffic. Antoni Sarcevics shot was deflected narrowly over just after the half hour with Eggert Jonsson volleying over the resultant corner from a few yards out when it looked easier to score.
The chances kept coming with Grant going close for a third time five minutes before the break but his miscued shot from the edge of the area went just the wrong side of the post.
With the wind the visitors started the second half brightly.
A more direct style saw a couple of long throws cause panic in the Fleetwood defence before Aaron Wildig sliced a shot wide of the target.
Fleetwood still posed a real threat though, Jonsson heading Grants corner onto the roof of Thompsons net on the hour mark.
It was just three minutes later when the hosts took the lead.
Ryan drove in on the right side of the area and fired a low ball across goal with Ball deflecting the ball home from six yards out just four minutes after coming on as a substitute.
The Shrimps were undeterred though with Paul Mullins free-kick from distance testing Chris Maxwell in the Fleetwood goal.
But as the visitors pressed gaps were bound to open up at the back and Henen nearly profited but after driving at The Shrimps defence his shot went narrowly wide.
Ball then came close to a second but was denied by Thompson's outstretched leg after breaking in behind with Henens follow up missing the target.
Bentleys side were well in the game though, Wildig again finding space to shoot wide as the search for an equaliser intensified.
Fleetwood continued to have the better of the openings however, Grant going close before the game was all but settled 15 minutes from time.
Grant robbed The Shrimps of possession 40 yards from goal and had a free run on goal, After he was denied by Laurence Wilson the ball broke for Ryan to fire past Thompson from 12 yards as Fleetwood players queued up for their chance.
Far from a Shrimps comeback, it was a Fleetwood third that looked more likely in the closing stages, Henens well struck shot from 30 yards hitting the side netting.
Kevin Ellison did have one excellent chance but was denied by Maxwell one-on-one as Morecambe's Wembley dream came to an end.
Fleetwood: Maxwell, McLaughlin, Pond, Davis, Bell, Jonsson, Sarcevic, Ryan (Haughton 87), Grant (Proctor 82), Henen, Fosu (Ball 59). Subs not used: Gogic, Teixeira.
Morecambe: Thompson, Edwards (Wilson 66), Dugdale, Parrish, Beeley, Wildig, Murphy (capt), Barkhuizen (Molyneux 80), Mullin (Devitt 66), Ellison, Forrester. Subs not used: Kenyon, Miller.
Booked: Ellison, Barkhuizen
Referee: Paul Tierney.