Anthony Wordsworth curled home a superb free-kick from the edge of the area to deny Uwe Rosler’s Bees the three points their performance deserved.
Clayton Donaldson had given the hosts the lead on 56 minutes, latching onto a Myles Weston throughball to cut in and curl home a beauty from 12 yards.
Brentford dominated from start to finish but were toothless in front of goal despite playing some impressive flowing football. Marcus Bean forced a reflex save from goalkeeper Mark Cousins and Niall McGinn flushed a string of efforts just wide of the upright.
Just before the break, Michail Antonio blazed wide for United, who were pinned back in their own half for long spells.
Their plight looked even worse when substitute John-Joe O’Toole saw red for a lunging tackle on Weston with eight minutes remaining. Jonathan Douglas forced a stop from Colchester’s keeper before Wordsworth had the final word on 90 minutes with an exquisite effort.