Mark Cousins was called into action early, getting down low to stop Sean Shield’s effort.
Dan Sparkes’ free kick was aimed towards Craig Robson at the far post, but it went beyond him and out.
Danny Kedwell’s shot was comfortable for Cousins 20 minutes in, 10 minutes later, Nathan Ashmore did well to palm Sparkes’ low free kick around the post.
Ephron Mason-Clark’s chest and volley went over the bar from the edge of the box, but on the stroke of half time the visitors took the lead.
Kedwell managed to turn on the edge of the box before finishing low into the bottom right corner.
The Bees had several half chances after the break as they looked to get back into the game. At the other end, Ebou Adams shot wide of goal from 25 yards out.
Ebbsfleet doubled their advantage in the 65th minute, Corey Whitely challenging Cousins one-on-one, the ball fell kindly to him in the second phase and he looped it in.
Shaq Coulthirst had his curling shot from 20 yards out saved before Sparkes’ powerful free kick was also saved.
The Fleet put the game beyond all doubt in the 89th minute, Sean Shields tapping home after former Bee Luke Coulson’s initial effort fell right into his path.
Barnet – Cousins, Alexander, Robson, Adams, Harrison (Barham, 80), Sparkes, Fonguck, Elito (Coulthirst, 61), Tutonda, Sweeney, Mason-Clark (Walker, 68)
Unused – Rihards Matrevics, Joe Payne
Attendance – 1,217 (321 Ebbsfleet)
Referee – Richard Hulme