New skipper Brian Wilson's first goal for nearly three years - seven minutes before the break - put the visitors on course for their first win in the competition for nearly five years.
But the League One side lost their way after the break and two goals in the space of 10 minutes put League Two Dagenham well on track to a famous triumph on their home turf.
Medy Elito cancelled out Wilson's sweetly struck free-kick with a 53rd-minute header.
Magnus Okuonghae was then sent off for the U's in the 63rd minute for a second yellow card for a clumsy foul on Zavon Hines, before defender Brian Saah added a second from close range little over a minute later.
Abu Ogogo netted his second goal of the season with 12 minutes remaining before substitute Louis Dennis - having been on the pitch for just 63 seconds - added a fourth for good measure as the home team completed a fine comeback.
Victory for the hosts was their first for four games while defeat for Colchester means they have now not won in their last four.
- Sports & Recreation
- Brian Saah