They were the Irishman's first goals for the Shrimpers since his move from Preston in early March and could be the most important in their season.
They did however all but end Macclesfield's faint hopes of automatic promotion and Brian Horton's men have now only taken three points from their last six games.
Macclesfield might have scored in the second minute when Matthew Tipton flicked on a Mark Bailey long throw for Jonathan Parkin to produce an acrobatic scissors kick that was spectacularly saved by Darryl Flahavan.
Southend then got into their stride with Luke Guttridge twice setting up Lawrie Dudfield only for the veteran to first mis-time a header and then slice a shot wide.
Paul Harsley then produced a snap-shot for Macclesfield with a half-volley from the edge of the box that flew inches over the bar.
The Silkmen took the lead in the 28th minute when a 25-yard free-kick from Parkin came back off the post for David Morley to follow in and score with a controlled shot from eight yards.
But their joy was short-lived, Dudfield's flick releasing McCormack to thump a low drive under Steve Wilson from the edge of the box.
Horton threw on forward John Miles at the break and he set up Parkin on 54 minutes but the big striker fired across the face of goal from the angle.
Southend looked dangerous throughout with Freddy Eastwood making Wilson save at his near post in the 57th minute before Guttridge volleyed over the bar on the hour.
Danny Swailes then missed a header for Macclesfield from six yards before McCormack lashed a drive just wide at the other end.
The 21-goal man Eastwood should have sealed it for the Shrimpers on 83 minutes but saw his shot bobble past the far post.
But McCormack made no mistake in the 89th minute when he exploded past Macc's static back four to arrow a clinical finish into the far corner.