Leading 3-2 from the first leg against their Essex rivals, The Shrimpers would have been confident that a solid performance at Roots Hall would book their ticket to Cardiff's Millennium Stadium next month.
However, the match did not get off to the best of starts for the home side as Kemal Izzet gave The U's a 1-0 second leg lead three minutes in.
However, the tie was decided just before the break, as Southend's Drewe Broughton equalised on the night for Steve Tilson's side.
Colchester were unable to restore parity to the tie in the second half and Southend's players celebrated at the final whistle, as they booked themselves into their first final in the club's 98-year history.
The Shrimpers will meet either Sheffield Wednesday or Blackpool in the final, with those two to play their Northern Area final second leg tie at Hillsborough next week.
Click below for match summary:
LDV Vans Trophy Southern Area final - second leg
Southend United 1-1 Colchester United (Agg: 4-3)
