The Shrimps have now only lost once in 16 games, keeping alive their faint hopes of making the final play-off places, whereas Macclesfield are still not mathematically certain of avoiding the drop.
The killer goal came in the 85th minute when giant centre-back David Artell converted Garry Hunter's corner with a towering downward header at the far post.
Morecambe had already had the ball in the back of the net three times, twice from first-half corners, but on both occasions Diarmuid O'Carroll was ruled to have blocked off keeper Jon Brain.
They again thought they had broken the deadlock in the 84th minute when Michael Twiss slid the ball across the six-yard line, only for Hunter to stroke home from an offside position.
Macclesfield's best chance came as early as the third minute, when Izak Reid picked out Gareth Evans at the near post, only for his neat header to fly inches wide of the upright.
They were again unlucky in the 20th minute when a rising shot from John Rooney flew inches over the bar. Centre-back Nat Brown was the next to go close with a far post header that flew wide.
Morecambe started the second half brightly with Stewart Drummond thumping a volley straight at Brain while Wayne Curtis saw a deflected drive from Shaun Brisley picked off by the Macc keeper.
Macc again went close when a free-kick from Lee Bell flew inches wide of the upright with Emile Sinclair inches away from making a vital touch.
Before Morecambe broke the deadlock a mistake from Paul Morgan allowed O'Carroll to set up Hunter, who powered a shot from the diagonal over the crossbar.