The Owls were held to a 1-1 draw yesterday afternoon as rivals Sheffield United won at Bramall Lane.
It means the second placed Blades move four points clear of the Owls who are third with only three games to go.
Ian Henderson put Colchester ahead with just three minutes gone and the Owls struggled to find any rhythm before the interval.
Henderson poked home from close range following a neat link-up in the penalty area with Steven Gillespie.
The Owls created few opportunities before the break but striker Nile Ranger was guilty of a horrible miss after good work on the flank by Michail Antonio.
Defender Miguel Llera scored for the third game in a row to level for the Owls after 51 minutes - tapping home from close range at a Chris Lines freekick.
But Colchester held on for the point which is unlikely to make any difference to their season.The two points dropped could be extremely cost to the Owls.