A goal by Manny Omoyinmi in the very last minute was enough to earn Margate a crucial point after a battling performance.
The visitors looked likely to go home empty-handed after being outplayed for large periods of the game.
But they kept battling and deserved to grab a point after refusing to admit defeat.
Exeter took the lead through leading marksman Sean Devine after half an hour.
Devine powered home a header from Kwame Ampadu's fine cross as Exeter made their first-half pressure count.
Gareth Sheldon had earlier twice gone close for the Grecians with long-range shots as the home side piled on the pressure.
Margate were pushed back for much of the first half and despite a few long range efforts from Omoyinmi they rarely threatened Exeter.
Les Afful blazed wide for Exeter after finding himself clean through on goal.
Glenn Cronin headed Scott Hiley's fine cross wide and Devine was denied by the goalkeeper, but Exeter were unable to extend their lead.
After the break the Grecians continued to create chances but struggling Margate also looked more of a threat going forward.
Omoyinmi struck the ball into the arms of the goalkeeper as Margate adopted a more positive approach and Exeter found themselves hanging on in a game which they should have put beyond the visitors.
They were made to pay the price in the 90th minute.
Chris Todd handled just outside the box and presented Margate with a dangerous free-kick. Omoyinmi made no mistake with a perfectly struck effort to earn his side a point.
The goal stunned Exeter who had no time to recover, but the Grecians only had themselves to blame for not finishing off the visitors and the result in the end was probably a fair result.