Early and late goals left the Clarets facing a long trip home from Essex empty-handed as Colchester ended their run of four successive defeats.
Michael Duff’s side did their best to hit back with a dominant second-half performance but couldn’t force an equaliser and were punished by a late second goal as they missed the chance to get off the foot of the Professional Development League’s northern group.
It needed a morning pitch inspection to get the game on after heavy overnight rain and the home side got off to the best possible start as they went in front inside five minutes when Tariq Issa was picked out at the back post by Ryan Gondoh to slot home.
Aiden O'Neill went close for the Clarets
Burnley had a chance to reply shortly afterwards when Dwight McNeil found Ntumba Massanka with a lovely lofted pass, but the forward could only force Dillon Barnes into a simple save.
Duff’s men came out raring to go in the second half and came close through substitute Tommy Wood, the striker heading Ali Koiki’s cross straight at Barnes in the United goal.
Minutes later, Barnes was in action again, keeping out close-range efforts from Aiden O’Neill and Christian N’Guessan.
Burnley, with four wins from their previous seven games, kept pushing for an equaliser and it looked as if they would get it just past the hour mark when McNeil again picked out Massanka at the back post.
Massanka teed up midfielder O’Neill, whose strike from 10 yards out was again well stopped by Barnes.
And with just a couple of minutes to go, substitute Decarrey Sheriff tapped the ball into an empty net after Issa’s pass had cut out goalkeeper Conor Mitchell to seal the points for the U’s, who repeated their home League Cup win over the Clarets and secured an eighth win in the league southern section.
Burnley: Mitchell, Clarke, Koiki, N’Guessan (Blair 86), Perkins, Younger, Chakwana (Bayode HT), O’Neill, Massanka, Goodridge (Wood HT), McNeil. Sub: Stone, Wilson.