The U's have been eliminated in the FA Cup first round by Marine AFC who beat Steve Ball's side on penalties after a 1-1 draw after extra time.
Steve Ball made two changes to the side that came out on top against Stevenage in the week.
Noah Chilvers and Omar Sowunmi came in to the starting eleven for Ben Stevenson and Tommy Smith, with Marley Marshall Miranda added to the bench.
It was a fairly even opening ten minutes with the home side content just to keep the ball.
Callum Harriott was on the end of a few challenges that left him holding the back of his left leg, and had to be replaced after eighteen minutes, with Josh Bohui coming on.
But the visitors took the lead after twenty minutes. A brilliant save from Gerken pushed Barrigan's free kick on to the post, with Anthony Miley quickest to react and tap the ball into the empty net.
The U's were looking to get back into the game, and were pushing bodies forwards, but with efforts from Pell and Sowunmi flying over the bar.
Gerken was called into action with five minutes left to play of the first half when Neil Kengni got around Bramall and forced a diving save from Gerken to keep the score at 1-0.
But Steve Ball's side were unable to find an eqauliser against the eighth tier side, trailing by a goal at the break to Miley's twenty-first minute goal.
The U's opted for a change of shape in the second period, with Tommy Smith coming on for Miles Welch-Hayes and heading to the left of a back three.
And it seemed to work for Colchester United when Harry Pell capitalised on a spilled ball from Bayleigh Passant. The Marine 'keeper spilled Chilvers' initial shot, with the U's skipper following in to direct the ball into the back of the net and equalise.
Kwame Poku nearly game the U's the lead a minute later when he bent a shot just wide of Passant's post with the 'keeper scrambling.
It seemed as though that was the best chance of the remainder of the ninety minutes for the U's, with Marine sitting deep and soaking up all the United pressure.
Marine had possibly the best chance of the last part of the game when James Barrigan was found alone at the back post, but only able to blast the ball high and wide into the back of the north stand.
Extra time was needed to sort the tie out, with an additional half an hour being played.
And the U's looked far the better side in extra time with Brown and Folivi linkng well up top and nearly adding that valuable second goal.
But neither side was able to find the breakthrough.
The game needed to be decided with a penalty shoot-out, and Marine stepped up to win with five perfect penalties.
Josh Bohui was the only Colchester United player to miss for the U's when he slid the fourth penalty wide, with Michael Howard winning the game for his side with the final penalty.
Colchester United starting XI: Gerken, Welch-Hayes (Smith 61), Bramall, Sowunmi, Senior, Pell, Brown, Harriott (Bohui 18), Chilvers, Eastman, Poku (Folivi 81).
Unused Subs: George, Cowan-Hall, Scarlett, Marshall Miranda.
Marine AFC starting XI: Passant, Solomon-Davies, Joyce, Doyle (Devine 86), Miley, Raven, Kengni, Hmami (Howard 82), Cummins (Strickland 105), Touray, Barrigan (Hughes 99).
Unused Subs: Mendes, Wignall, Shaw.