The only goal of the game came after 76 minutes from the penalty spot as Leon Clarke fired home his fourth goal in successive games since joining the club on loan from Charlton.
It came after he himself had been brought down in the box by Matt Heath and finally broke the deadlock in a game that looked destined to remain goalless.
At the opposite end Scunthorpe were indebted to their keeper Sam Slocombe for two fines saves.
In the first half he went full stetch to his left to keep out a 20-yard effort from midfielder Gavin Massey.
And in the 57th minute he did even better with a brilliant reaction save to block out a close-range header from Clinton Morrison.
It left Colchester still without a win in eight games.