In truth, Charlton should have been out of site long before Joe Howe scored a consolation goal in stoppage time.
The Addicks fielded six players with first team experience, and they had another two on the bench.
Cristian Ceballos showed some superb touches, and the defence was barely troubled all night. More than an hour had gone before the hosts had their first meaningful attempt on goal.
Charlton sewed the game up in two incredible minutes in the first half. After 35 minutes, the hugely impressive Ceballos’ thunderbolt screamed into the net from 30 yards.
Two minutes later, a slick move down the right saw the ball played into the middle. George Lapslie exchanged passes with Zak Ansah before guiding the ball into the net from close range.
Karlan Ahearne-Grant, Ansah, Harry Lennon, Ceballos and Lapslie all had opportunities during the game, but the Addicks could not increase their lead.
There were no further goals until added on time when, surprisingly, it was Fleet who found the net to pull one back.
Howe converted a right-wing corner, but the visitors had no further scares before the referee blew the whistle for full time.
Charlton will now face Dartford in the final of the competition.
Ebbsfleet: Miles; Boulding, Miller-Neave, Pooley, Denny; Atkinson, Holmes, Howe, N’Guede; Atomonyogo (Dabove 58), Johnson.
Subs (not used): Della Valle, Nouse, Tagg, Stewart.
Goal: Howe 90.
Subs (not used): Beeney, Kennedy, Moore.
Goals: Ceballos 35, Lapslie 37
Referee: Simon Finnigan (Kent).
Attn: 630.