Southend substitute Jim Corbett shot the Blues in to the second round of the LDV Vans Trophy at Layer Road last night from the penalty spot.
The striker converted the Shrimpers' fifth spot-kick with his first touch of the ball after coming off the bench in extra time, to end the U's hopes of avenging their Southern Area Final exit at Blues' hands last season.
Corbett beat Colchester keeper Aidan Davison from 12 yards after U's skipper Wayne Brown blasted wide.
Southend took the lead through a fierce Tes Bramble shot after 36 minutes.
But Richard Garcia levelled for the hosts in the 63rd minute to set up extra-time.
Full match report and pictures in tonight's Echo
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