Louis Lancaster's Youth Team pushed league leaders Colchester close before eventually losing 3-2 at Florence Park.
The Bees took the lead through Josh Stockwell's 25 yard effort before Macauley Bonne equalised to send the two sides in level at the break.
Sub Courtney Senior re-established the lead on the hour before Bonne and Jack Simmons scored twice in 10 minutes to condemn Brentford to a fourth straight defeat.
Full match highlights are available here for Bees Player subscribers.