A penalty thirty minutes from time won and taken by Michael Folivi earned Dave Huzzey and Richard Hall's side a valuable three points in the Professional Development League.
The young U's picked up their first win of the year against QPR on Tuesday afternoon, with a slender 1-0 win after Michael Folivi converted from the penalty spot.
After the first half had ended goalless, the U's took their chance to take the lead when Folivi who has been left out of the first team for the last couple of games stepped up to put his side ahead.
Also in the side were Josh Doherty and Josh Bohui who have been given minutes in the U23s squad to maintain their fitness going into the second half of the season.
With the three points, the U's move ahead of their opponents in the league, now sitting in seventh place while QPR slip down to eighth. Colchester United are now level on points with Watford, only sitting behind the Hornets on goal difference, although the Vicarage Road side have played two games less.
Next up for the U's youngsters is another trip on the road, this time to Charlton Athletic in a week's time.
U's: Coulter, Tchamadeu, Akolbire, Terry, Doherty, Marshall Miranda, Cornish, Bohui, Sayer, Folivi, Tovide, Hutchinson, Tricker, Hasanally, Johnson, Trialist.