The scoreline didn't do justice to a City side who could have won by a hatful.
Only poor shooting from good positions and a couple of fine saves from home keeper Dean Gerken kept the score down.
Brian Tinnion's side always had more inventiveness than lacklustre Colchester who were mostly restricted to half chances.
City's first-half dominance continued into the second 45 minutes and two fine finishes by skipper for the day Stephen Brooker and England under-21 striker Leroy Lita were enough to earn them three points.
Brooker might well have had a hat-trick. His goal was the former Port Vale striker's 15th of the season. He also struck the crossbar with a fine dipping volley in the first half and once in each half dragged powerful shots across the goal and just beyond the far post.
Brooker was the star man, wearing the captain's armband for the first time for a much-changed City.
But manager Tinnion will have been pleased with a performance full of good things - especially the debut of teenager Dave Cotterill on the right wing and Tom Doherty who dominated in midfield.
It was a mystery how the game remained 0-0 at half time.
Colchester had a couple of good opportunities, both falling to Neil Danns the former Blackburn player.
Early on he rounded the goalkeeper after a through ball from Stephen Hunt but saw Danny Coles block his effort on the goal line.
And shortly before half time, Steve Phillips saved an effort from a cross coming in from the right from Kevin Watson.
City had two had good opportunities but Lita was off target from the penalty area and Cotterill mis-kicked his first effort when he was unmarked in front of goal.
Meanwhile, Luke Wilkshire missed an open goal when he should have hit the target.
The visitors continued to control the game in the second half and once the first goal came from Brooker the result never looked in doubt.
Colchester's best effort was a clever free-kick from Greg Halford which curled just over the corner of post and crossbar.
There was a late flurry of bookings after Colchester substitute Guylain Ndumbu-Nsungu and Doherty clashed.
It had never been a dirty game but Danns and Craig Fagan also picked up bookings.