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Ebbsfleet will take a one-goal lead into the second leg of their play-off semi-final against Whitehawk on Sunday.
Victory in Brighton on Wednesday night was just reward for an excellent away performance although the tie remains in the balance thanks to a late Whitehawk goal.
Fleet led 1-0 at half-time through Stuart Lewis and a Danny Kedwell free-kick put them further in front before Danny Mills pulled one back.
There was no place for Tom Bonner in Ebbsfleet's starting XI, the club captain dropped to the bench alongside Jordan Parkes. Kenny Clark and Dean Rance returned after injury and suspension respectively while Dean Pooley and Joe Howe retained their places at full-back.
Matt Fish missed out with an ankle injury while Bryan van den Bogaert has returned to his native Belgium for family reasons. Kedwell skippered the visitors.
John Paul Kissock and Aaron McLean were left out of the squad altogether while Michael West and Alex Osborn - having just completed loan spells with Whitehawk - were among the other Fleet players who watched from the stand.
Liam Graham took Osborn's place in the only Whitehawk change.
Ebbsfleet survived an early scare when Nick Arnold's deep free-kick from the left found Dave Martin unmarked at the far post. Fortunately for the visitors, his header back across goal dropped wide.
Former Whitehawk midfielder Sam Deering cut inside Arnaud Mendy at the other end and was fouled, sparking an angry reaction from several Fleet players. Mendy was cautioned and Deering's free-kick, meant for Matt Godden, eventually dropped for Kedwell but his sliced effort flew well wide.
At the other end, Fleet keeper Nathan Ashmore got behind a Jake Robinson shot from distance but Fleet were starting to come into the game as an attacking force.
Godden sent a header looping over and then saw a low shot creep past the left-hand post after Kedwell had knocked the ball down for him just inside the box.
The visitors hit the front on 28 minutes with a goal of real quality. A move started by Rance saw Godden release Kedwell down the right and his clever pull-back was turned into the net via the far post by Lewis, arriving late in the box.
It might have been 2-0 moments later when Kedwell spotted a gaping hole in the Hawks defence, although his through-ball for Godden was a touch too heavy.
Martin lashed a shot out of the ground and Graham went into the book for sending Anthony Cook flying on the touchline.
Referee Andrew Laver had his yellow card out again moments later when Godden took a tumble on the edge of the Hawks box. Fleet's leading scorer looked to have been clipped but Mr Laver decided he had taken a dive.
Godden squared for Kedwell a minute before the interval but Whitehawk managed to scramble the ball behind for a corner.
Seven minutes into the second half, Cook found himself in behind the Hawks defence but Craig Ross stood up well to make a crucial save.
Cook then hooked the ball down the left touchline and Godden was in, with only Ross to beat, but a heavy touch allowed the goalkeeper to come out and gather.
Whitehawk started to build pressure and Howe had to be alert to divert Martin's left-wing cross away from Mills inside the six-yard box.
Godden hooked a first-time shot over the bar from Deering's pass and Cook sent a curling effort well wide of the far post but Whitehawk then came within inches of equalising.
Rance slipped 20 yards from his own goal and Nick Arnold burst into the gap, rattling the near post with Ashmore beaten.
Moments later, it was 2-0. Torres earned himself a caution for bringing down Cook and Kedwell lashed the free-kick past Ross, who got hands to the ball but couldn't keep it out.
But the Fleet's lead was halved eight minutes from time. Ashmore got down well to save from Torres but the rebound ran for Mills and he rifled the ball home.
Charlie Sheringham came on for Godden and almost made it 3-1 when he latched onto Kedwell's pass and tried to round Ross, but the keeper made another crucial intervention.
Five added minutes saw Whitehawk throw everybody forward but the Fleet held on to preserve their slender advantage.
Whitehawk: Ross, Graham (Sessegnon 80mins), Rents, M'Boungou, Rose, Mendy (Ijaha 73mins), Arnold, Torres, Robinson, Mills, Martin. Subs not used: Fraser, Gargan, Gotta.
Ebbsfleet: Ashmore, Pooley, Howe, Lewis, Acheampong, Clark, Deering, Rance, Kedwell, Godden (Sheringham 87mins), Cook. Subs not used: Miles, Bonner, Parkes, Shields.
Attendance: 1,055 (319 away).