Courtney Senior’s first-half goal was enough to inflict defeat upon Morecambe at the Globe Arena.
The midfielder struck his third of the campaign moments before half-time to settle a closely-fought game.
Morecambe boss Jim Bentley had made two enforced changes to the side which won at Carlisle United seven days earlier.
Injuries to Rhys Oates and Andrew Tutte meant Jordan Cranston and Kevin Ellison were restored to the starting XI.
A Colchester side lying in the top six were always going to be a good examination for the in-form Shrimps and they certainly posed some difficult questions early on.
Harry Pell sent a diving header off target and Kane Vincent-Young flashed a shot over the bar inside the opening five minutes as the visitors began well, prompted by the ever-threatening Ryan Jackson.
Pell saw another effort from distance comfortably held by Barry Roche but, after their difficult start, Bentley’s players began to assert themselves.
Vadaine Oliver’s run into the area was ended by a jarring challenge with Frankie Kent, which ended with both men on the floor and in need of treatment.
Liam Mandeville’s optimistic long-range effort was off target and Oliver’s touch was too heavy as the Shrimps broke from a Colchester corner.
However, the deadlock was broken with half-time approaching when Morecambe lost possession and Colchester worked the ball beautifully for Senior to slot the ball past Roche.
Instead of dropping their heads, Morecambe came out for the second half and took the game to their visitors.
One penalty appeal for apparent handball came to nothing, two through balls were marginally too heavy for A-Jay Leitch-Smith and Ellison chipped off target with keeper Rene Gilmartin closing him down.
Cranston and Luke Conlan were off target with shots from distance but the best chance fell to Oliver, who headed against the bar from Zak Mills’ cross.
In contrast, Colchester’s breaks were more sporadic, though Jackson again showed his threat to lead a counter, leave Conlan on the floor and cross for Frank Nouble, whose header was well blocked by Josef Yarney.
Back play switched to the other end with Oliver and Leitch-Smith having shots blocked, proving the story of Morecambe’s afternoon; they huffed and they puffed but they could not breach the visitors’ resolute rearguard.
Morecambe: Roche, Mills, Lavelle, Yarney, Conlan, Wildig, Cranston, Mandeville, Leitch-Smith, Ellison, Oliver. Subs not used: Halstead, Oswell, Mendes Gomes, Brownsword, Piggott, Hedley, Codjovi.
Colchester United: Gilmartin, Eastman, Prosser, Kent, Jackson, Pell, Lapslie (Comley 87), Vincent-Young (Dickenson 77), Senior (Collins 72), Nouble, Norris. Subs not used: Barnes, Wright, Mandron, Kensdale.
Referee: Andy Haines.