A first half header from Tommy Smith was enough to give the U's all three points on their way back to Essex, as Steve Ball's men defend excellently to seal the win.
Steve Ball named a lineup with one change from the weekend win against Grimsby Town, with Miles Welch-Hayes coming in for Junior Tchamadeu at right back after the sixteen-year-old's debut at the weekend.
It was a cold and wet evening at the Sands Venue Stadium, with the U's looking for their first win on the road this season.
But the hosts had the best chance of the opening exchanges as Green was arriving at the back post for a driven cross. Had it not have been for the brilliant defensive work of Miles Welch-Hayes, the Scunthorpe wide man would have had an easy tap in, but the U's man intervened and shiielded the ball to Dean Gerken.
Other than that early scare, there was little action to speak of for the first twenty-five minutes of play at the Sands Venue Stadium, but the U's got themselves ahead just before the half-hour mark.
Tommy Smith stayed up from a free kick that was cleared, before the ball was recycled out to Cohen Bramall who saw the U's captain in the centre of the area and picked him out with a fine cross. Smith calmly headed the ball into the back of the net with Howard unable to do anything about the goal.
The hosts rallied before the break though and could quite easily have been level with five minutes of the half remaining. It was a corner routine that caught the U's out, with the ball eventually reaching Alfie Beestin, but his low effort was scuffed and Gerken pulled off a great save to retain the lead for the visitors.
And Gerken was called into action once more before the teams headed for the shelter of the dressing rooms. In first half stoppage time, Gerken punched away an effort from Beestin once again before the U's defence was able to clear.
The home side came out raring to go in the second half and really started to apply the pressure to the U's goal, forcing Gerken into yet more saves.
The second half sub of Ryan Loft almost had an instant impact as he got his head to the ball in the area, but a diving save from Gerken kept the U's lead, before Devarn Green went closer still with a curling effort that bounced off the outside of the post.
Scunthorpe thought they had scored ten minuted into the half when Gerken palmed the ball on to the bar from Loft's effort with the ball bouncing on the line and Tommy Smith clearing the ball brilliantly before it had crossed the line.
And the heroics kept on coming from the visiting 'keeper when he denied Loft yet again, this time stopping a low driven effort that was aiming for the bottom corner.
The U's didn't get forwards much but they did create a chance down the right flank with Bramall and Senior combining to get a in towards Norris. Unfortunately the U's front man slipped at the vital time, and couldn't convert.
The home side kept pressing, and really applied the pressure as time went on, but save after save from Gerken, and block after block from the back line looked to have sealed the win for the visitors.
A final attempt at an equaliser came in injury time of the second half, with Eisa lurking at the back post from a Beestin cross. A brave header from Miles Welch-Hayes got the ball clear and the U's were able to hold on for a first away victory of the season.
It is three points that move the U's into the play-off places, now sitting sixth with twenty-seven points, level on points with fifth place Exeter, but trailing on goal difference.
Next up for Steve Ball's men is another away trip, as United head to Port Vale on Saturday looking to make it three wins in a row, and consolidate their top seven space.
Scunthorpe United starting XI: Howard, Clarke (Rowe 77'), McGahey (Bedeau 42'), Omariase, Gilliead, Green (Eisa 74'), Jarvis, Spence, Beestin, Taylor (Loft 46'), O'Malley.
Unused subs: Watson, Hallam, McAtee.
Colchester United starting XI: Gerken, Welch-Hayes, Bramall, Smith, Senior (Clampin 71'), Norris (Poku 71'), Brown (Folivi 59'), Harriott (Sownmi 53'), Chilvers, Eastman, Gambin.
Unused subs: George, Marshall Miranda, Tchamadeu.