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Ebbsfleet will face Whitehawk in the National League South play-off semi-finals.
Daryl McMahon's side head to Brighton for the first leg on Wednesday night after the Hawks clinched fifth place with a 3-0 win away to promotion rivals Hemel Hempstead.
Elsewhere on Saturday, Matt Godden scored his third hat-trick of 2015/16 as Fleet beat Eastbourne 4-2 at Stonebridge Road, the striker's treble taking him to 30 goals for the season.
Ebbsfleet came into the game already guaranteed to finish second in the table so McMahon made four changes to his starting XI. Dean Pooley and Joe Howe replaced full-backs Matt Fish and Bryan van den Bogaert, who were left out of the squad altogether.
Sam Deering came in for JP Kissock in midfield while there was a start for Anthony Cook at the expense of Sean Shields. Academy player Ollie Boulding made the bench.
Eastbourne were captained by former Fleet defender Craig Stone and their team also included Nathan Collier - once of Dartford.
Anthony Acheampong was cautioned inside six minutes for catching Elliott Romain late but the home side bossed things early on.
Danny Kedwell burst into the box and saw his powerful shot pushed behind for a corner following good work by Stuart Lewis and Deering down the Fleet right.
Deering was involved in the opening goal on 12 minutes. He spread play wide to Howe and when he in turn found Cook, the winger's low cross was palmed out by goalkeeper Lewis Carey to the waiting Godden, who found the roof of the net with a controlled finish.
It was almost 2-0 two minutes later. Jordan Parkes caught out Carey with a free-kick from wide on the left and the keeper was relieved to see the ball strike the near post.
Fleet had to switch to 3-5-2 when Pooley pulled up injured and was replaced by Kissock.
Parkes sent a swerving shot just over the bar before Eastbourne's first effort on goal saw a Stone shot trickle wide after Gavin McCallum's free-kick had dropped at his feet.
Darren Lok's header from a Jack Evans delivery looped over Fleet keeper Nathan Ashmore and dropped just wide of the far post but the home side had soon doubled their lead.
Kedwell's ball from the left was turned inside the near post by Godden, who had almost nodded home a Cook cross moments earlier.
Balls into the box looked Eastbourne's best route to goal as Ebbsfleet dominated in open play. Evans delivered a corner from the right and Romain sent a header wide before Evans failed to hit the target with a volley from 20 yards.
Godden almost helped himself to a third goal on the stroke of half-time, turning Bouwe Bosma but dragging his right-footed shot across the face of goal and wide.
Some shaky Ebbsfleet defending at the start of the second half offered Eastbourne hope.
Howe was knocked off the ball on the byline and Jake Sheppard's low cross was fired wastefully over the bar by Evans.
An injury to Cook saw Boulding sent on for his league debut but it was a Sports substitute, former Fleet loanee Nathan Pinney, who made an instant impact. The striker had been on the pitch for less than a minute when he ran through and put the ball into the net at the second attempt.
Carey held a low Deering shot at the other end and Kedwell fired into the side netting but for a while, it was Eastbourne doing all the pressing and Ebbsfleet on the back foot.
Kedwell's long-ranger forced Carey to concede a corner, from which Deering had a low shot blocked, but the visitors were level 20 minutes from time.
More iffy defending was punished by a powerful Pinney shot which flew past Ashmore.
Charlie Sheringham was sent on with 15 minutes to play and he followed Pinney's lead by changing the game almost immediately. Deering's curling free-kick from wide on the right was just begging to be converted and Sheringham obliged with a thumping header.
Godden lashed a brilliant shot past Carey to complete his treble and then saw another effort blocked after Howe had picked him out with a neat cutback.
Eastbourne were on the ropes in the closing stages.
Sheringham combined with Kedwell and his fizzing cross was only just taken off Godden's toe.
Mesmeric link-up play between Godden and Sheringham saw the latter shoved but no penalty given before Sheringham controlled Kedwell's cross in stoppage-time only to slash his volley into the Plough End.
Ebbsfleet: Ashmore, Pooley (Kissock 18mins), Howe, Lewis, Acheampong, Bonner, Deering, Parkes (Sheringham 72mins), Kedwell, Godden, Cook (Boulding 52mins). Subs not used: Miles, McLean.
Eastbourne: Carey, Sheppard (Pinney 51mins), Khinda-John, Evans, Stone, Buckley, McCallum, Collier, Lok, Romain, Bosma (Taylor 46mins). Subs not used: Worrall, Worthington, Haysman.
Attendance: 1,348.