Carlisle started well with Kallum Higginbotham and Joe Garner both going close, but Cumbrians goalkeeper Mark Gillespie denied Anthony Wordsworth, Craig Eastmond and Jabo Ibehre.
Colchester took a 25th-minute lead through Eastmond, who interchanged with Sanchez Watt before tapping in from close range before Carlisle felt they should have had a penalty when Higginbotham appeared to have been shoved in the area by Brian Wilson.
Ibehre doubled the U's lead just after the half-hour when he converted first-time from four yards following Watt's fine low cross.
Gillespie denied Marcus Bean and Watt clipped the post before Peter Murphy's header came back off the crossbar for Carlisle just before half-time.
Carlisle started the second half brightly and Higginbotham, Mike Edwards and James Berrett all missed free headers, while Ibehre fired just wide for Colchester, who claimed their fourth league win out of five under new boss Joe Dunne.