Guiseppe Sole's second-half penalty ensured Ebbsfleet ended a three-game winless run against bottom side Lewes.
Relegated Lewes went ahead when Josh Jirbandey volleyed home from a corner five minutes before the break.
But in first-half injury time the hosts responded when Charlton loanee Rashid Yussuff struck from 25 yards.
And with 19 minutes remaining Sam Fisk fouled Sole in the penalty area, the striker picking himself up to condemn Lewes to a 32nd defeat this season.
Ebbsfleet United: Cronin, Stevens, Crooks, Charles, Opinel (Pooley 36), Yussuff, West (Sole 59), Ricketts, Long, Gash (Ibe 88), Shakes. Subs Not Used: Mott, Purcell.
Booked: Charles, Ricketts, Opinel.
Goals: Yussuff 45, Sole 71 pen.
Lewes: Banks, Barness, Breach (Hall 50), Jirbandey, Fisk, Wheeler, Standing, Keehan (Osborne 46), Rooney, Storrie, Rivers (Sutton 79).
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Subs Not Used: Foreman, Bell.
Booked: Barness, Rooney, Fisk.
Goals: Jirbandey 41.
Att: 1,098
Ref: S Burt (Northampton).
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