Substitute Manny Panther was the Grecians' goal hero with a superb 85th-minute strike to earn his side an excellent draw.
It was a point that seemed a long way away at the start of the second half when the visitors, who had been outplayed in the first half, were reduced to ten men when Bertrand Cozic was sent off for an alleged elbow on Morecambe's Craig Stanley.
But ironically it was a decision that changed the pattern of the game in City's favour, as Morecambe lost their previous fluency and Exeter came far more into the game.
The home side made a bright start and were almost ahead in dramatic fashion in the third minute when the on-loan Danny Carlton flashed a left footer inches wide of the left-hand post.
Then Stewart Drummond floated a header just over from Ryan McGivern's cross as the Shrimps roared forward. And McGivern himself had a golden chance to convert Carlton's cross but took too long to get his shot away and Exeter cleared the danger.
Drummond then forced Paul Jones to make a superb save from a close-range header before the Shrimps took a deserved lead on 22 minutes when Daniel Seabourne's back-pass was under-hit and Rene Howe nipped in to score with a simple tap-in.
But despite all the pressure and play, the Shrimps just had the one goal to show for their efforts.
When Cozic saw red on 48 minutes, Morecambe looked home and dry - but Exeter had other ideas.
Steve Basham almost equalised after breaking past the lethargic McGivern, and Ryan Harley fired wide from 30 yards. Morecambe defender Ryan McCann then produced a fine tackle to stop another Harley run into the danger zone.
Exeter received their just rewards when Panther curled home a sweet goal as David Artell and McGivern dozed on a break.
The Grecians then came close to sealing a remarkable victory in stoppage time when Adam Stansfield latched on to a long throughball but shot straight at Barry Roche when he should have scored.