Andy Drury gave the hosts an early lead with a close range on seven minutes, before the Fleet bagged a second four minutes before half time through Danny Kedwell’s header.
A great strike from Dayton two minutes from time gave Orient a lifeline, but they were unable to force an equaliser in stoppage time.
On the back of last weekend’s 2-1 FA Cup defeat to Gillingham, Head Coach Steve Davis made five changes to the starting XI. Dan Happe and Mark Ellis returned in central defence, James Brophy took up the left wing-back position while Alex Lawless and Matt Harrold were also handed starts.
The O’s also welcomed Jobi McAnuff back to the bench following a toe injury, though were without striker Macauley Bonne for the first time this season with the 22-year-old away on international duty with Zimbabwe, and defender Joe Widdowson who served a one-match suspension.
With the match live on BT Sport, both sides impeccably observed a minute’s silence as everyone in attendance paid respect to those who lost their lives in war. We Will Remember Them.
It was the O’s who got the game underway and enjoyed a large amount of possession during the opening minutes, with a James Brophy cross being cleared away at the far post by Ebbsfleet’s Kenny Clark.
Despite this, Ebbsfleet made the most of their first chance to open the scoring after seven minutes when Andy Drury poked home from close range.
The reaction to falling behind was positive from the O’s, as they controlled possession and really should have been level on the 13th minute when Matt Harrold connected with a Jake Caprice cross only to see his effort come back off the post before James Dayton was beaten to the follow-up.
Dayton then saw a shot from the edge of the area blocked by Clark seconds later, and Harrold was once again denied as the 20 minute-mark approached as his header was tipped over the bar by Nathan Ashmore.
Harrold’s header proved to be the final chance for the best part of 15 minutes as neither side managed to create much in the final third, but with four minutes of the half remaining Ebbsfleet doubled their advantage through captain Danny Kedwell as he powered a Myles Weston cross beyond Charlie Grainger.
Luke Coulson looked to add a third a minute later with a speculative effort from distance which was held by Grainger.
Three minutes stoppage time was shown by the fourth official and the O’s almost clawed a goal back when David Mooney latched onto a Grainger ball up field, but his chipped effort was held by Ashmore for the final action of the half.
Following the interval, Orient made one change as Romuald Boco came on in place of Dan Happe in a move that saw a change in formation as the O’s switched to a 4-4-2 diamond.
In a similar fashion to the first the O’s were controlling a lot of the possession, but failing to trouble Ashmore in the hosts goal and with 25 minutes remaining made their second change as Jobi McAnuff replaced Alex Lawless.
Grainger was then called into action for the first time in the second half on the 68th minute as he dived well to his left to push a Weston corner around the post for a corner which was eventually cleared.
Not long after Kedwell released strike partner Coulson with a pass in behind the defence, but despite breaking into the penalty area the forward was denied by Mark Ellis who tracked back brilliantly to slide in cleanly and claim the ball.
With 10 minutes left on the clock Myles Judd replaced Caprice for the O’s final change, before Coulson drilled a shot over the bar for the hosts.
Frustrated by the lack of chances in the Ebbsfleet third, McAnuff then fired a shot from distance which flew over the bar.
The O’s were handed a lifeline on the 88th minute however, as midfielder James Dayton pulled a goal back with a rasping strike from the edge of the box to beat Ashmore and set up a nervy final few minutes.
With three minutes stoppage time shown Orient threw bodies forward in search of an equaliser, and Brophy showed great footwork to beat several players before being wiped out by a sliding challenge. Advantage was played however as the ball ran through to Mooney who could only fire at Ashmore as the hosts held on for the three points.
EBBSFLEET: Ashmore, Magri, Mambo, Clark, Connors, Weston (Shields 87), Rance, Drury, Cook, Coulson (Powell 89), Kedwell (C)
SUBS: McCoy, Miles, Bubb
GOALS: Drury (7), Kedwell (41)
ORIENT: Grainger, Caprice (Judd 80), Ellis, Sendles-White, Happe (Boco HT), Brophy, Lawless (McAnuff 65), Westbrooke, Dayton, Mooney (C), Harrold
SUBS: Sargeant, Clay
GOALS: Dayton (88)
BOOKED: Lawless (5)
REFEREE: Adrian Quelch
ATTENDANCE: 2,021 (463 Orient supporters)