It was an exciting battle of affairs as the two sides went into the break level, but the entertainment continued late into first half added time as Anthony Cook was given a straight red card following a late challenge on Josh Rees which also saw Michael Spillane react.
The visitors took advantage of their numerical advantage on 55 minutes when Bagasan Graham drove forward before smashing into the bottom corner from long-range.
But two goals three minutes apart from the hosts meant the Clarets were beaten by the Fleet at Stonebridge Road.
Chelmsford City Boss Rod Stringer made two changes to the side that beat Dartford 2-1 to reach the Vanarama National League South final: Michael Spillane and Graham both started for the Clarets as Josh Hill and Luke Daley were demoted to the substitutes bench.
Ebbsfleet came close to carving open the visitors in the opening ten minutes, however Aaron McLean was adjudged marginally offside from Danny Kedwell’s through-ball.
The Clarets came close to scoring after thirty minutes when Robbie Willmott’s corner met Mark Haines at the far post. However, the central defender could only force a fine save from Nathan Ashmore from close range.
City saw their chance continue as the ball bobbled around the box in a shaky few seconds for the hosts, but Graham could not quite direct a shot goal-bound.
The visitors continued pressure into the final few minutes of the half but could still not capitalise on their ascendancy.
But the Clarets were handed a numerical advantage when Whistler Richard Hulme brandished a red card to former City player, Cook. The speedy full-back lunged in for a challenge on midfielder Josh Rees and the referee had no option but to dismiss the defender for his reckless challenge.
Dickson had a great chance to put City ahead in the opening minutes of the second half, but the experienced striker could only watch as his shot forced a save from the out-stretched Ashmore.
The hosts then had a chance of their own moments later when Sam Deering ingeniously turned two defenders, but he had his long-range shot grabbed well by Ross Fitzsimons.
But City eventually took advantage of their numerical and possessional advantage on 55 minutes. Graham collected the ball from thirty yards, drove forwards before unleashing a powerful shot into the bottom corner of Ashmore’s goal.
The hosts went in search for an equaliser but Deering’s trickery in the final third could not muster anything.
But Fleet’s determination eventually came through as Winfield rose highest in a crowded box to head home following the home side’s multiple chances from set-pieces.
And the hosts went ahead minutes later as substitute Darren McQueen slid home from just a few yards to erupt Stonebridge Road into noise.
City boss Stringer threw the dice twice as he introduced substitutes Luke Daley and Anthony Church for Shaun Jeffers and Josh Rees as he went in search for an equaliser.
But the Clarets could not quite muster up any more chances and the whistle soon signalled the end of an agonising defeat for the visitors.
1. Nathan Ashmore
2. Anthony Cook
3. Jack Connors
4. Marvin McCoy
5. Dave Winfield
6. Kenny Clark
7. Dean Rance
8. Andy Drury
9. Danny Kedwell ©
10. Aaron McClean
11. Sam Deering
12. Yado Mambo (84’, on for Sam Deering)
13. Jonathan Miles
14. Jack Powell (46’, on for Danny Kedwell)
15. Sean Shields
16. Darren McQueen (71’, on for Dean Rance)
1. Ross Fitzsimons
2. Mark Haines
3. Bagasan Graham
4. Max Porter
5. Chris Bush ©
6. Michael Spillane
7. Robbie Willmott
8. Josh Rees
9. Louie Theophanous
10. Chris Dickson
11. Shaun Jeffers
12. Elliott Buchanan (88’, on for Bagasan Graham)
14. Anthony Church (83’, on for Josh Rees)
15. Josh Hill
16. Luke Daley (83’, on for Shaun Jeffers)
17. Lamar Johnson
Ebbsfleet United: Josh Rees (75’)
Chelmsford City: Michael Spillane (45+1’)
Ebbsfleet United: Anthony Cook (45+1’)
Chelmsford City: None.
Ebbsfleet United: Dave Winfield (72’), Darren McQueen (75’).
Chelmsford City: Bagasan Graham (55’).
Half Time Score: Ebbsfleet United 0-0 Chelmsford City
Full Time Score: Ebbsfleet United 2-1 Chelmsford City
City Man of the Match: Josh Rees