It has taken the Sky Blues six matches to wipe out their 10-point deduction for going into administration and they leapfrogged Notts County, also on one point, by virtue of a better goal difference.
Colchester were missing key players such as Freddie Sears and Sanchez Watt and as a result were dominated from start to finish.
Leon Clarke twice hit the woodwork in the first half as well as drawing two fantastic saves from U's goalkeeper Sam Walker.
It looked like the hosts might regret their inability to convert when Alex Gibley volleyed over 10 minutes before half-time.
But Wilson opened the scoring two minutes later, tapping in a close-range rebound following Blair Adams' long-range shot to settle any nerves.
The division's top scorer doubled Coventry's lead in the 57th minute when he rounded the goalkeeper to slot into the empty net after a neat exchange of passes with Clarke.