Michael Ricketts set Walsall on the road to victory with his 12th goal of the season after Colchester wasted good early openings.
Jamie Guy was twice played clean through on goal but could not beat keeper Clayton Ince on either occasion.
Ricketts then drilled the ball home from close range after good work from Alex Nicholls and Sofiene Zaaboub.
Troy Deeney doubled the lead with a looping header past Jimmy Walker after Ricketts set up the opportunity.
Walsall: Ince, Palmer, Weston (Smith 36), Gerrard, Boertien, Nicholls, Hughes, Bradley, Zaaboub (Taundry 81), Ricketts, Deeney (Williams 68). Subs Not Used: Gilmartin, Ibehre.
Goals: Ricketts 17, Deeney 42.
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Att: 3,719
Ref: Graham Salisbury (Lancashire).
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