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Dover made it back-to-back National League wins for the first time since September on Saturday.
Michael Woods' first-half stunner proved enough for Andy Hessenthaler's men as Ebbsfleet's struggles continue at the wrong end of the table.
Dover, fresh from their Boxing Day win over Bromley, started well and striker Inih Effiong headed wide Josh Passley’s right-wing cross.
Whites took a 14th-minute lead when Jack Munns played the ball into Effiong, who set up Woods for a first-time strike into the top corner from the edge of the box.
Fleet struggled to retain possession in the opening stages, Gozie Ugwu was left isolated in a 4-5-1 formation with little support getting to him.
Ugwu shot over from distance, Tyler Cordner turned the ball wide from a corner and Myles Weston’s free-kick found the side netting.
It took until two minutes before half-time for Ebbsfleet to register a shot on target as Jack King’s downward header from a Weston free-kick was comfortably gathered by Whites keeper Yusuf Mersin, who was playing with Lee Worgan ruled out by concussion.
Both Dover full-backs found their way into referee Declan Bourne’s notebook, Josh Passley for time-wasting on 26 minutes after taking an age - not for the first time - to take a throw-in and Bobby-Joe Taylor for kicking the ball away.
Ugwu escaped punishment for a similar offence moments later but Frankie Sutherland was booked in the first half after a pull back on Ricky Modeste, the Fleet midfielder showing his frustration after being dispossessed as he lined up a shot.
Fleet improved after the break and could have levelled it up on 53 minutes. The offside flag stayed down and Ugwu went clean through, opting to decline the chance to lob Mersin and instead try to round the Whites keeper, who got down smartly to save at the striker’s feet.
The hosts lost Weston to injury before the hour mark while Dover introduced former Folkestone forward Ade Yusuff for the last half-hour.
Substitute John Goddard went close to an equaliser with 21 minutes left when his near-post effort was deflected wide.
Ayo Obileye’s 20-yard volley was tipped behind at the near post brilliantly by keeper Mersin and then Jai Reason headed Tyler Cordner’s effort from the resulting corner off the line.
Yusuff shot wide eight minutes from time with Dover’s first attempt at goal in the second half and a series of corners in stoppage time helped them run the clock down - Obileye's shot going weakly at goal just before the final whistle went.
Ebbsfleet: Holmes, Ekpiteta, King, Cordner, Weston (Goddard 56mins), Payne, Obileye, Sutherland (Umerah 77mins), Blackman, Reid (Adeloye 77mins), Ugwu. Subs not used: Palmer, Grimes.
Dover: Mersin, Passley, De Havilland, Lokko, Taylor, Woods, Reason, Munns (Yusuff 59mins), Modeste (Rigg 72mins), Effiong, L’Ghoul (Jeffrey 68mins). Subs not used: Simpson, Cumberbatch.
Attendance: 1,222 (205 away).