Bees striker Charlie MacDonald sealed the points in the 15th minute when he dived full-length to head home John Bostock’s pin-point cross from the right.
Home goalkeeper Wojciech Szczesny kept his side in it with two brave saves, first to deny Kevin Lisbie and then Kayode Odejayi in the first half.
Brentford dominated possession with some slick passing football in a contrast of styles to Colchester’s more direct approach to big strikers Clive Platt and John White.
Brentford’s Ben Strevens went close with a half-volley just before the break and MacDonald almost threatened to add to his tally with a low angled drive.
The visitors almost snatched an undeserved point in injury time when Platt’s long-range effort forced a full-length save from the Bees goalkeeper.