Simon Weaver’s Town have barely drawn breath since promotion and registered a ninth win of the campaign in Kent.
They had Howe to thank once more, the defender heading in a 30th-minute corner from Joe Leesley who now has 10 assists for the season.
Myles Weston volleyed over for Ebbsfleet in response, while Howe hit over at the other end.
Aaron Williams then added a second off George Thomson’s 72nd-minute pass, scoring for the second game in a row as Harrogate maintained their unbeaten away record.
Elsewhere, three goals in the first 50 minutes saw FC Halifax Town slump to a 3-0 defeat at Aldershot.
Goals from Adam May and Adam McDonnell put Aldershot 2-0 up at half-time, a score which flattered the hosts.
But any plans Town had of getting back in the game were shattered when Jake Gallagher added a third just after the break.
Aldershot took the lead amid a decent start by Halifax, who saw more of the ball, and looked more comfortable with it than the hosts.
But The Shots gobbled up their first chance when May swept in Gallagher’s low cross from the right after he was fed by McDonnell’s through ball.
And McDonnell was then on the end of the next cross into the Halifax box by Matt McClure with a controlled finish at the far post.
Nathan Clarke should have halved the deficit when he met James Berrett’s free-kick, but headed across goal at the far post.
Jacob Hanson and Ryan Sellers were two of Town’s best attacking outlets when both full-backs marauded down the flanks; from a Sellers cross, Dayle Southwell glanced a header wide.
Aldershot would have made it a surely insurmountable 3-0 just before the interval but for Sam Johnson’s terrific save to tip over May’s superb shot from 25 yards.
But Johnson was culpable in Aldershot’s third just three minutes after the restart when he punched a cross straight to Scott Rendell, who then found Gallagher, who looped at header across goal and in.
Southwell saw a shot cleared off the line after going round keeper Cole, while Jordan Preston, who hobbled off in added time with what looked like a possible hamstring injury, hit the woodwork from six yards at a tight angle with just over 10 minutes remaining.