The Rebels had led this Fifth Round match at Stonebridge Road, but were unable to hang on - and suffered a 3-2 defeat.
It was an awful start for the Rebels as they went behind after only nine minutes. Set piece specialist Lee Protheroe whipped in a corner and captain Paul McCarthy headed home from close range.
Within three minutes though, the Rebels replied in some style. Michael Murphy picked up the ball outside the area and hit a dipping half-volley which beat former Rebel Paul Wilkerson emphatically, hitting the underside of the crossbar on its way into the net.
Joy soon turned to misery though as Darron Wilkinson was forced to withdraw from the game, after aggravating his hamstring injury once again, and was replaced by Glen Harris.
It looked as though the home side were set to go in front midway through the half when a cross looked set for Roy Essandoh to head in, but superb defending by Ian Hodges, in his role as makeshift centre-back, kept the former Wycombe striker at bay.
In the second half it was the Rebels who took a shock lead after a foul on Josias Carbon gave Slough a free kick. Christian Metcalfe laid the ball off to Michael Murphy, who powered a left-footed shot past the outstretched hand of Wilkerson - who seemed to react too late - to give Slough the lead, much to the delight of the 200 or so travelling supporters behind the goal.
It was a lead the away side could not hang on to though, and four minutes later Gravesend equalized when the dangerous Jay Saunders was left unmarked in the six-yard box to shoot past Allaway.
There was now only one side looking likely to win, and it was a matter of seeing if the Rebels could hold onto a replay - but when former West Ham forward Manny Omoyinmi beat Hodges, he raced through the Slough defence, and coolly slotted the ball past Allaway to break Slough hearts and ultimately give Gravesend victory.
Slough were unable to fashion an equaliser in the remaining 20 minutes – but the Rebels can hold their heads high after a tremendous run in a season in which they have become famous as ‘cup specialists’.
Ebbsfleet United Line up
Paul Wilkerson, Justin Skinner, Graham Porter (Lee Gledhill), Manny Omoyinmi, Paul McCarthy, Steve McKimm, Jay Saunders, Roy Essandoh (James Pinnock), Lee Protheroe, Matthew Lovell, Andy Drury (Moussa Sidibe). Subs not used: Jimmy Jackson, Masters.