Alek Przespolewski scored the only goal of the game for Havant, who also knocked the Fleet out of the FA Trophy in January.
And with the sides having played out a goalless draw on the opening day of the Skrill South season, Steve Brown's side have now failed to score in more than four hours of football against the Hawks.
Ebbsfleet were missing Osei Sankofa and Michael West through injury, so Anthony Acheampong partnered Yado Mambo in central defence and Michael Thalassitis started up front.
It was a game of few chances, settled on 76 minutes when Przespolewski - who'd only been on the pitch for two minutes - collected Pedro Monteiro's knock-down and rifled a shot beyond Preston Edwards.
Ebbsfleet remain fourth in the table although Kent rivals Dover, who are eight points back in fifth, now have two games in hand.
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