Grays' second win over Ebbsfleet within a week moved the Essex club out of the bottom four in the Blue Square Premier.
The visitors started brightly but Stuart Thurgood lashed in for the hosts from 25 yards in the 31st minute.
Ishmael Welsh doubled their advantage five minutes after the restart with a drilled effort from the left.
Ebbsfleet substitute Kezie Ibe stabbed in after 73 minutes but defender Jamie Stuart condemned the Kent side to their fifth straight league defeat late on.
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