First-half goals from Toumani Diagouraga and Aaron Wildig saw the Shrimps leapfrog their visitors in the table and move eight points clear of bottom club Stevenage.
Derek Adams had made one change to the Morecambe side which drew with Mansfield Town last time out.
Illness meant that Carlos Mendes-Gomes was left out altogether with Saturday’s goalscorer, Alex Kenyon, back in the starting XI.
With the windy conditions making the play something of a lottery, the Shrimps had the breeze in their favour during the opening 45 minutes.
The first chance fell on nine minutes when Cole Stockton was found inside the area, where he worked half-a-yard of space and saw his shot pushed away by Macc keeper Jonathan Mitchell.
Kenyon’s dipping shot went over but the respite was temporary as Morecambe took an 18th-minute lead.
A long throw into the box wasn’t cleared by the visitors and Diagouraga lashed home the loose ball.
Adam Phillips tried to catch out Mitchell with a wind-assisted 35-yarder but failed to make sufficient contact.
He should have scored just after the half-hour when Diagouraga sent him through, only to put his shot into the side netting.
It was 2-0 10 minutes before half-time but, from the visitors’ point of view, it came in a contentious fashion.
They were convinced a throw-in should have been theirs, only for the decision to go Morecambe’s way.
They capitalised when the resulting throw reached Wildig, whose shot took a wicked deflection and wrongfooted Mitchell.
John O’Sullivan was inches wide from 20 yards as the Shrimps sought a third goal before the break.
In contrast, the Silkmen were forced into a game of containment before they could enjoy the benefit of the conditions.
Their only real chance in the first half had fallen to Arthur Gnahoua after Morecambe failed to clear a corner but he scooped a shot over when he should have hit the target.
In response, they made two changes at half-time with Ben Tollitt and Theo Archibald brought on.
Tollitt could have scored within five minutes of his introduction, heading over from a corner after Macc had seen a penalty appeal for handball waved away.
With the visitors trying to push forward at every opportunity, another corner ended with the ball dropping to Connor Kirby, who could only shoot wide when well placed.
Whitehead came closer with a shot from distance that Mafoumbi fumbled to safety but, despite their possession, clear chances were at a premium for the visitors.
Another substitute, Donovan Wilson, saw a header easily collected by Mafoumbi, who had to push over Kirby’s long-range attempt.
Morecambe’s chances were more fleeting with O’Sullivan blazing over from the edge of the box but their game management ensured they were never in serious danger of conceding.
Four minutes of added time came and went with little in the way of alarm as the Shrimps could celebrate a job well done.
Morecambe: Mafoumbi, Cooney, Old, Lavelle, Cranston, Kenyon, Phillips, Diagouraga, O’Sullivan, Wildig (Conlan 81), Stockton. Subs not used: Halstead, Bradbury, Brewitt, Mbulu, Slew.
Macclesfield Town: Mitchell, O’Keefe, Kelleher, Horsfall, Fitzpatrick, Hamblin (Tollitt 46), Tracey (Wilson 68), Kirby, Whitehead, Gnahoua (Archibald 46), Ironside. Subs not used: Blyth, Rose, Cameron.
Referee: Michael Salisbury.