Stoke had not conceded a goal in the last 656 minutes but they were trailing after just 75 seconds at Layer Road as Jamie Cureton slotted home the first of his two early goals.
City were stunned as Cureton's instinctive 20-yard chip took a slight deflection off a defender to loop over keeper Steve Simonsen and drop under the bar.
It was a blow from which Stoke never really recovered. They had countless chances to score in the first half but their shooting let them down badly. In fact their finishing was woeful all afternoon.
Cureton showed them how to do it by doubling the lead for Colchester in the 17th minute. Richard Garcia, starting his first match for nine games following an ankle injury, moved forward for livewire Cureton to prod home from eight yards out.
It was Cureton's 12th goal of the season. He and his strike-force partner Chris Iwelumo have now scored 22 goals between them this term.
Stoke should really have scored themselves before the break. Their leading scorer, Ricardo Fuller, blazed horribly over the top on a couple of occasions, while Aston Villa loanee Lee Hendrie also sliced wide from some excellent positions.
The anticipated Stoke rally never happened in the second half and it was their Essex hosts who completely bossed the game. In fact, they could have scored more than their eventual total of three goals.
The killer third goal arrived in the 62nd minute when Garcia headed powerfully home from Chris Barker's deep cross from the left wing. It was Garcia's fourth goal of the campaign and it wrapped up the points for United.
Having lost their first four league games of the season, Colchester have made giant strides up the table over the last three-and-a-half months. They have now leap-frogged Stoke to sit in the top six of the Championship for the first time in the club's history.
For Stoke, this was a day to forget. They had won six and drawn the other of their previous seven matches, but will they need to sharpen up on their shooting if they are to mount a promotion push this season.