Exeter City lost their 1-0 lead to a late goal at St James' Park on Saturday, when Manny Omoyimni curled in a 90th minute free kick.
City had worked hard and Sean Devine put them a goal ahead in the 32nd minute, but for their dominance, they were unable to find a second, and when Chris Todd handled outside their box following Margate's best 15-minute spell, the former Oxford striker put away their final chance.
City now travel to Dagenham and Redbridge next Saturday.
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