The Shrimps bowed out of the FA Cup as two first-half goals earned League One high-fliers Shrewsbury a third round tie.
Jim Bentley’s side once again played some neat football and enjoyed a large share of possession but were ultimately undone by two goals in five minutes.
Morecambe were always the underdogs against a side second in League One at the start of play and they were almost undone in only the second minute.
Alex Rodman found himself in space down the left-hand side but drilled a shot from a tight angle against the foot of the post with Bary Roche beaten.
From there Morecambe held the home side comfortably and the game flowed from end-to-end without any real chances.
But the Shrimps were then hit by a double blow that would ultimately give Shrewsbury victory.
Right winger Shaun Whalley found space down the right and after getting past Patrick Brough fired in a low cross that Rodman turned past Roche from six yards out.
Five minutes later Rodman turned provider with a long ball forward for Jon Nolan who beat the Morecambe defence to the ball but was brought down by Barry Roche for a clear penalty.
Whalley stepped up to send Roche the wrong way and the tie had changed beyond all recognition.
For all their nice football the Shrimps rarely troubled the home defence in the first period but were a different proposition after the break.
Vadaine Oliver and Aaron McGowan came off the bench and Morecambe looked more of a threat.
Garry Thompson and Adam Campbell put in early crosses that caused problems for the home defence and Adam McGurk had a chance to threaten but shot wildly wide from 30 yards.
Thompson forced MacGillvray into a decent save on 67 minutes and Oliver volleyed over a minute later.
The Shrimps’ best chance came three minutes from time when Callum Lang was played in on goal but saw his effort well saved by MacGillvray who raced well from his goal to cut down the angle.
A goal at that stage may have made things interesting but in the end Shrewsbury played the game out to clinch the win.
Shrewsbury Town: MacGillvray, Bolton, Nsiala, Beckles, Sadler, Godfrey (Dodds 59) Whalley (C Morris 80), B Morris, Nolan, Rodman (Gnahoua 70), Payne. Subs not used: Gregory, Riley, John-Lewis, Adams.
Morecambe: Roche, Lund, Old, Muller, Brough (McGowan 46), Fleming, Kenyon (Oliver 46), Wildig, Thompson, Campbell (Lang 78), McGurk. Subs not used: Nizic, Rose, Osborne, Winnard.
Referee: Craig Hick.