Colchester boss Geraint Williams, who used to be a season ticket holder at Cardiff as a schoolboy, masterminded United's sixth home victory on the trot. It was only the Bluebirds' third league defeat of the campaign.
After a quiet first period the game burst into life early in the second half when striker Kevin Campbell, who was enjoying his first start for Cardiff, rattled the bar with a shot from eight yards out.
That was a lucky escape for Colchester, but within a minute, they had gone down to the other end to break the deadlock themselves, thanks to a smart finish from Kevin McLeod.
Greg Halford was the creator with a good cross from the right. Jamie Cureton was closed down before he could shoot, but Johnnie Jackson was able to slide the ball into the path of McLeod who made no mistake with his left foot from eight yards out.
It was McLeod's second goal for the club, and his second in successive weekends.
He had scored his first on his full debut against Southampton the previous weekend, but this was a special goal against Cardiff, because he used to play for their Welsh rivals Swansea.
Cardiff had not been at their best, but they still managed to poach an equaliser in the 66th minute with man of the moment Michael Chopra bagging his 11th goal of the season.
Colchester defender Pat Baldwin could not clear substitute Willo Flood's cross, and there was the alert Chopra to sweep home the loose ball in to an unguarded net.
That equaliser prompted a spell of Cardiff pressure, but the Essex side weathered the storm and then scored two late goals to secure what was a deserved victory.
Substitute Jamie Guy put Colchester back in to the lead in the 83rd minute, seven minutes after coming on as a substitute. The U's teenager shrugged aside the challenge of Darren Purse to beat keeper Neil Alexander with a low shot into the far corner of the net. Guy had been put through by Kemal Izzet.
The U's made the game safe in stoppage time when another substitute, Ritchie Jones, was dragged down in the box by Stephen McPhail. Referee John Moss immediately pointed to the spot, and sent off McPhail because he was the last man.
Leading scorer Cureton fired home the penalty low to Alexandra's right to chalk up his eighth goal of the season, and to put the seal on another home win.
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