Colchester booked their place in the next round of the Johnstone's Paint Trophy at the expense of Gillingham.
The visitors were the best side in the first half and striker Clive Platt somehow headed over after 24 minutes with the goal gaping.
But Mark Yeates grabbed eventual winner on 60 minutes when he curled a superb left-foot shot past keeper Simon Royce.
The home side piled on the pressure but Colchester held on and Gillingham were booed off by their fans at the end.
Gillingham: Royce, Fuller, King, Mills, Nutter, Southall, Weston, Bentley, Jarrett (Richards 81), Jackson (Pugh 75), Barcham (Murphy 74). Subs Not Used: Kiely, Lewis.
Booked: King, Bentley.
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Goals: Yeates 60.
Att: 1,557
Ref: Fred Graham (Essex).
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