Padraig Amond's first goal for Morecambe earned his side a second successive home win.
The former Accrington striker fired a sweet volley past Luke McCormick seven minutes from time to give the Shrimps their first win over Plymouth in the Football League.
Jim Bentley's side had to come from behind after Plymouth took the lead through a Reuben Reid penalty in the 28th minutes.
Morecambe skipper Mark Hughes was adjudged to have hauled down Marvin Morgan in the Morecambe box and Reid stepped up to send Barry Roche the wrong way from the spot.
The Shrimps equalised almost immediately through their talisman Kevin Ellison. The veteran chased down a a loose ball on the edge of the Plymouth area and smashed the ball past Luke McCormick from 12 yards.
The second half saw few chances but Plymouth went close when Roche was forced into a stunning save low to his left to block Curtis Nelson's header before Andy Parrish produced a vital clearance from Neal Trotman's follow up.