Lee Brown and Scott McGleish ensured Bristol Rovers secured their third consecutive win under Mark McGhee.
Brown opened the scoring, tapping in an Eliot Richards cross that was touched on by McGleish.
Rovers were then awarded a penalty, which was duly despatched by McGleish, after Danny Carlton tugged Matthew Lund's shirt.
Jordan Burrows then missed a chance for the Shrimps but Kevin Ellison fired in the rebound.
Both sides hit the woodwork in the first half with Morecambe's Phil Jevons striking the post and McGleish rattling an upright with a glancing header.