Aaron Pressley and one of the Trialists grabbed the goals in the second period to confirm the win for the resolute Bees.
There was a change of shape for Brentford B in order to cater for a number of defensive injuries, with Ben Hockenhull, Kane O'Connor, Tristan Crama and Aubrel Koutsimouka all currently recovering from injuries.
A back three of Fin Stevens, Ethan Robb and Lewis Gordon kept The Blues out for much of the game with their goal coming from a set piece midway through the second period.
It was a first half in which the young Bees dominated in terms of possession, as well as chances. Inside the first 10 minutes The Bees looked dangerous, particularly with the hard-working Pressley holding the ball up well and feeding the likes of Alex Gilbert and the wide players in Lachlan Brook and Valgeir Valgeirsson.
A good chance came on 11 minutes when Pressley's running eventually saw him find Brook out on the left, and his cross towards Mogensen was snuffed out by the home side before the young Dane could get a clean effort away at goal.
A Mogensen strike from distance would go over the host's goal before Fin Stevens went very close when he fired from distance low across goal from the right, but the ball went agonisingly wide on 36 minutes.
The best chance then came for The Bees a few moments later when a good cross in from the right saw Pressley unmarked, and despite connecting well, the Chelsea keeper pulled off a smart save. The ball could only rebound into the path of the onrushing Gilbert, who also struck well, but for another fine stop from The Blues' keeper.
Chelsea's most threatening moment came on the cusp of half-time when Stevens was on hand to block fantastically after a powerful effort from close range from Bryan Fiabema.
The second half was just 10 minutes old when The Bees took a deserved lead when one of the Brentford Trialists did well down the left before crossing into the box and Pressley netted his 13th of the season with an accurate header to make it 1-0.
Substitute Sam McClelland managed to level things just three minutes later from a set piece where an accurate free-kick found the Chelsea man, who headed home an effort which left Nathan Shepperd with little chance of keeping out.
The rhythm of the game when perhaps began to stem from the hosts, but for all of their possession in the middle of the pitch, and in defence, they were rarely able to trouble the back line of Robb, Gordon and Stevens.
The energetic Bees kept up their pressing game and carried a threat on the counter whenever they won back possession. The all-important goal came from that pressing on 80 minutes when one of the Trialists chased down the Chelsea keeper before he managed to dispossess him and tap home into an empty net.
The side continued to manage the final moments and prevented a late onslaught from the hosts with excellent game management in the latter stages.
Brentford B: Shepperd, Stevens Gordon, Robb, Trialist (Trevitt, 59) Valgeirsson (Trialist 88), Carre (Trialist, 75) Pressley (Trialist, 88) Gilbert (Trialist, 75) Mogensen (Trialist, 63) Brook (Hercules, 75)
Subs not used: Thompson, Winterbottom