Goals from Aaron Pressley, Alex Gilbert and Joe Adams gave the side the win in a match they dominated for large parts.
The young Bees named Luka Racic in the starting line-up as he stepped up his return from injury, whilst the likes of Mads Bidstrup, Lewis Gordon and Fin Stevens were involved after being part of the First Team match day squad on Tuesday night.
It was a game that Brentford B were alive to right from the off, and they had their first real chance when Bidstrup beat a couple of United players on the edge of the box before dragging his low effort just wide of goal.
That preceded the opener on 12 minutes when some good build-up play set Valgeir Valgeirsson away down the right before he crossed low for Pressley to notch his 18th of the campaign.
The Brentford number nine was denied again on 20 minutes with a similar attempt from close range, but for a good stop by the Ebbsfleet keeper. Ryan Trevitt also had a good chance whilst Gustav Mogensen saw his low effort from distance well collected.
United tested Nathan Shepperd for the first time around the 30-minute mark when Jack Paxman connected well with an effort from distance which the young keeper was equal to. Brentford B were then forced into a change on 34 minutes after Mogensen picked up a knock following a heavy United tackle as Alex Gilbert came on to replace him.
The second period saw much of the same and it took the side eight minutes to create a chance when Gilbert linked up well with Bidstrup, who turned cleverly, but his low effort was wide of goal.
It was so close to 2-0 on the hour mark as the relentless running of Bidstrup almost paid off with a goal as he chased the Ebbsfleet keeper before blocking the clearance. The ball then bounced towards goal but spun away off the line as the keeper managed to dive and collect whilst breathing a sigh of relief.
The game then swung in a couple of minutes when Stevens had a chance to score himself after being found out on the right in acres of space before he drove inside the box and fired an effort into the side netting. Just moments after that, United fortunately became level when Adams played a ball back which caught Shepperd out, and the Welshman was unable to readjust as it ended up in the back of the net.
The side then showed fantastic attitude to go back ahead as Gilbert had another effort 13 minutes from time before he then found the net a couple of minutes later. Great play down the right saw Adams cross low for Gilbert, who held his position around the penalty spot, before converting well into the bottom left-hand corner.
Adams then made the game safe when he moved out to the right, and though it looked like an excellent crossing position, his effort into the box ended up in the top corner at the near post to make it 3-1.
Brentford B: Shepperd, Stevens (Robb, 83) Gordon, Trevitt (Trialist, 70) Racic (Trialist, 45), Bidstrup (Trialist, 83) Valgeirsson, Pressley (Trialist, 58), Adams, Mogensen (Gilbert, 39), Brook (Hercules, 70)
Subs not used: Thompson
Ebbsfleet United: Firth, Chapman, Solly, Kahraman, Paxman, Trialist, Adebayo-Rowling, Wood, Poleon, Bingham, Trialist
Subs: Eirich, West, Trialist