Substitute James Keene scored deep in injury time to snatch all the points for visitors Bournemouth.
Keene broke the deadlock in the second minute of added time when he bundled home Stephen Cooke's cross.
It was a disappointing end for Colchester, who created a number of match-winning chances throughout.
Chris Iwelumo had their best chance, hitting the woodwork late on, while Bournemouth had a penalty appeal turned down when James Hayter fell in the box.
Colchester: Davison, White, Brown, Chilvers, Stockley, Halford, Izzet, Watson, Danns, Yeates (Williams 68), Iwelumo.
Subs Not Used: Baldwin, Gerken, King, Richards.
Bournemouth: Stewart, Cooper, Gowling, Young, Hart, O'Connor, Browning, Surman (Cooke 75), Stock, Foley (Maher 89), Hayter (Keene 89).
Subs Not Used: Rodrigues, Pitman.
Goals: Keene 90.
Ref: R Booth (Nottinghamshire).