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Ebbsfleet's play-off hopes were ended by Dover on Easter Monday.
Fleet needed a win to keep the pressure on seventh-placed Eastleigh but a goal from Alfie Pavey gave their Kent rivals all three points in the derby.
This result means the two sides will meet in the National League again next season.
Ebbsfleet were missing Jack King and Dave Winfield so Chris Bush stepped inside to partner Sam Magri at centre-half. Jack Payne replaced Ebou Adams in midfield and Gozie Ugwu was passed fit to play up front, with Michael Cheek dropping to the bench.
Dover, already safe from relegation and looking to finish in mid-table, made four changes. One of those saw Pavey picked ahead of Inih Effiong up front, while the return of Scott Doe in central defence allowed captain Mitch Brundle to move forward into midfield.
The home side came flying out of the traps, playing with lots of energy and pushing Dover back into their own defensive third.
Ugwu had a shot blocked after Danny Kedwell had nodded down Lawrie Wilson's cross and a surging run took Bagasan Graham past two players but he delayed his cross from the left and that allowed Whites to clear.
Kedwell almost cushioned another Wilson diagonal ball into Andy Drury's path, although Fleet were saved by the offside flag when Pavey volleyed home Anthony Jeffrey's cross from the left.
Jeffrey looked increasingly dangerous for the visitors and it took an excellent saving tackle by Magri to stop the winger in his tracks moments later.
Kedwell forced an excellent reaction save from Lee Worgan in a crowded penalty area before Nathan Ashmore matched him at the other end, getting down well to stop Bobby-Joe Taylor's free-kick sneaking inside the near post.
Dover were enjoying a good spell and Jeffrey's low cross from the left narrowly eluded Pavey in the middle after he'd skinned full-back Wilson.
The home side left several players unmarked when Taylor curled over a free-kick from the right and were relieved to see Brundle's powerful header ruled out for offside.
Ebbsfleet couldn't get out of their own half, though, and Dover kept creating chances. Brundle almost forced home another Jeffrey cross and Kevin Lokko fired wide from a Jamie Allen ball in before Jai Reason headed Jeffrey's left-wing delivery over the bar.
Ugwu powered past Taylor at the start of the second half but failed to pick out a team-mate with his cross and the Whites then came within inches of taking the lead.
Pavey picked out Brundle in space on the edge of the box and when Brundle gave him the ball back, Pavey whipped a shot beyond Ashmore only to see the ball crash back off the crossbar.
But the visitors deservedly took the lead on 51 minutes when Pavey touched home a terrific low cross from Jeffrey.
Fleet had a little spell of pressure and Worgan did well to grab the ball after Kedwell's deep cross had dropped for Graham.
Dover, though, looked dangerous every time they went forward and only Magri's last-ditch tackle stopped Jeffrey scoring from Reason's pass.
The home side, with Cheek now on the pitch for Ugwu, piled men forward knowing they needed to score quickly to keep their season alive.
Graham fired over when picked out by Kedwell, who then glanced a header just wide from Jack Payne's left-wing free-kick.
A tame effort by Drury was easily gathered by Worgan before Jeffrey lashed a wild effort over at the other end after Reason had helped the ball on.
Jeffrey almost rounded Ashmore moments later and then skied the ball from close range after substitute Inih Effiong had guided Josh Passley's low cross into his path.
Fleet had to go gung-ho in the closing stages, with Corey Whitely supporting Cheek and Kedwell up front.
As a result, they were wide open at the back and when Dover broke three-on-two, Pavey whipped a shot wide from Effiong's pass.
Ebbsfleet ran out of ideas in the end, Whitely lashing a late shot over as their hopes of a top-seven finish disappeared with a whimper.
Ebbsfleet: Ashmore, Wilson, Magri, Bush, Weston, Rance, Drury (Whitely 72mins), Payne, Graham (Adams 81mins), Kedwell, Ugwu (Cheek 58mins). Subs not used: Miles, Moncur.
Dover: Worgan, Passley, Lokko, Doe, Taylor, Brundle, Lewis, Reason, Allen (Effiong 64mins), Jeffrey, Pavey. Subs not used: Walker, Adebowale, Nortey, Daniel.
Attendance: 1,723.