Scunthorpe were rarely in the hunt in the opening stages, but improved as the game progressed troubling keeper Aidan Davison on a couple of occasions, and he was forced to make some excellent saves.
Matt Sparrow and Andy Keogh were key workers in the home side with Steve Foster doing an excellent job at the back.
Colchester skipper Karl Duguid put in a lot of work at the heart of their defence, while the lanky Greg Halford was dangerous at set pieces and his height was invaluable.
Colchester were first to settle and Mark Yeates forced an opening for Tony Thorpe whose shot struck Paul Musselwhite on the knees and was cleared.
Yeates then fired the ball across the face of goal following a corner, with no one on hand to follow up.
Scunthorpe's first chance came after 22 minutes, skipper Andy Crosby speared in a free-kick which was so high it crashed against the score board.
Sparrow then whipped in a free-kick from the left and Keogh managed a neat flick which was diverted wide.
The visitors hit back with Yeates meeting Gary Richards' free-kick but causing no trouble for Musselwhite. They followed that up with a Kevin Watson free-kick which Halford headed over the top.
Ian Baraclough then swung in a corner from the right for the Iron and Foster's header was narrowly wide, before Davison pushed away Keogh's shot following a surge forward by Michael Rose.
Referee Paul Taylor was busy before the interval making three bookings in quick succession as tempers flared. Scunthorpe's Sparrow and Foster saw yellow while Colchester's Thorpe saw the same colour, but was lucky to escape red for what appeared to be a head butt.
The second half saw Scunthorpe take a more attacking role with Cleveland Taylor twice going close from positions wide on the right.
Sparrow forced Davison into a couple of saves, while a Keogh flick on and a superb free-kick by Richard Hinds tested Davison.
In the last minute Clarke had the ball in the net, but his effort was in vain following the raising of a flag which did not please the Colchester players.