It had been a quiet start to the game. Craig Fagan shot a few yards over in the fifth minute, and the Tigers' Jason Price had a deflected shot held by Gerken three minutes later.
In the 17th minute, Andy Dawson curled a 20-yard shot a couple of yards over, and things were still pretty even.
But Fagan's downward header in the 23rd minute - the first shot on target for Colchester - was a sign of things to come. The Us' took the lead minutes later, when a slip by Michael Keane allowed Greg Halford to time an excellent pass to Gareth Williams, who put a powerful 20-yard shot from the left wing underneath City keeper Bo Myhill.
And just after the half-hour mark, the U's were 2-0 up after a well-worked set-piece, which saw Fagan poke the ball in straight from Kevin Watson's corner.
Colchester came out to attack in the second half, and did not look to sit back on their lead. They had a minor scare in the 53rd minute when Price nodded across goal, and although Gerken looked to have diverted it away from the net, only a goal kick was given.
Myhill was lucky to stay on the field after handling outside the area in the 81st minute, though the referee, probably taking into account the wet and slippery surface, only booked the City keeper after he had slid outside the box with the ball.
Peter Taylor, seemingly with no answers left, threw on youngsters Scott Wiseman and Russell Fry in the 64th minute, but neither made a real impact.
Danny Allsopp shot well over after a cross by Wiseman in the last five minutes and Junior Lewis put a header just wide in stoppage time, but the game had long since drifted out of the Tigers' grasp.