Southend hold a narrow lead in the LDV Vans Trophy Southern Area Final after winning the first leg with 10 men.
Thomas Pinault smashed in the opening goal for the home side but Tes Bramble set up Leon Constantine to level.
Drewe Broughton headed in and Bramble's
shot squirmed through Simon Brown's
hands to give the Shrimpers a 3-1 lead.
Broughton was then sent off for a
second bookable offence but even though Wayne Andrews headed one back the visitors still left with an advantage.
Colchester: Brown, Stockley, Alan White, Chilvers, Tierney, Duguid, Pinault, Izzet, Keith, Vine, McGleish.
Andrews, Bowry, Halford, McKinney.
Southend: Flahavan, Jupp, Cort, Warren, Stuart, Constantine, Hunt, Maher, Gower, Broughton, Bramble.
Subs: Emberson, Pettefer, Wilson, Steven Clark, McSweeney.
Referee: G Laws (Tyne & Wear).