After an even first-half, Halifax conceded for only the second away game in seven this season through substitute Sean Shields, who added another later in the half.
Halifax started like a team who had won six of their last eight games, hungry for the ball, looking lively when they had it and working hard when they did not.
Josh Macdonald showed a great turn of speed to produce a run and cross early on which Adam Morgan met with a first-time shot that was parried away.
Sam Johnson then kept out a rasping shot by the nippy Darren McQueen after he had latched on to a long ball forward.
Matty Kosylo struck the post after cutting in on his right-foot, then Johnson was called upon to keep out home captain Danny Kedwell’s shot from a tight angle.
Ebbsfleet did not have to work particularly hard to take the lead, with the outstanding Shields allowed to cut in on his right-foot by Cliff Moyo before Johnson was beaten at his near-post by the low shot.
By the time Shields added his second, a mirror image of his first as his low shot, this time from the right, flashed past Johnson at his near post, there was no way back for the Shaymen, who are down to 10th place, even though they are only three points adrift of leaders Dover Athletic after 13 matches.
If anything, Ebbsfleet, who are up to 12th, could have added more goals.
Ebbsfleet United: Ashmore, Magri, Clark, Bush, Connors, Weston, Rance, Powell, Drury (Shields 42), Kedwell, McQueen (Coulson 77). Unused substitutes: McCoy, Miles, Mills.
FC Halifax Town: Johnson, Moyo (McManus 81), Brown, Hotte, Wilde, Macdonald (Charles 64), Oliver (Clarke 32), Lynch, Kosylo, Morgan, Denton. Unused substitutes: Nicholson, Tomlinson.
Referee: D Rock.