The Bees took a fourth-minute lead when Marcello Trotta controlled before emphatically firing in from close range after Clayton Donaldson had nodded down at the far post.
Things went from bad to worse for Colchester six minutes later when defender Josh Thompson was dismissed for denying a goalscoring opportunity when he brought down Donaldson on the edge of the penalty area.
From the resulting free-kick Adam Forshaw planted a well-placed shot past Colchester goalkeeper Mark Cousins to leave Brentford in control.
Colchester pulled a goal back midway through the first half through 17-year-old Drey Wright, who picked up Kem Izzet's pass before advancing towards goal and stroking in a low shot past Bees goalkeeper Richard Lee.
And just before half-time Bees midfielder Tom Adeyemi was sent off after picking up his second yellow card in the space of 10 minutes.
But with five minutes remaining Harlee Dean tapped in from two yards after Cousins had failed to hold the ball to wrap up the points for Brentford.