Goals from debutant Conor Grant and Andy Williams saw Doncaster Rovers win Darren Ferguson's first home game in charge.
On-loan Everton midfielder Grant curled home a sublime effort to break the deadlock late in a first half that saw Colchester register more attempts on goal.
There was never any chance of Rovers just sitting back on their lead and they capped a confident second half display when a counter attack was rounded off by Williams.
Rovers were indebted to Thorsten Stuckmann for a string of good saves in both halves as United threatened to go ahead and then refused to lie down after the interval.
The game saw skipper James Coppinger equal Colin Douglas's all-time Rovers appearance record of 468, while Sir Alex Ferguson was at the Keepmoat Stadium to watch his son's new team in action.
Ferguson junior made two changes to the personnel beaten at Millwall, dropping Richie Wellens and Luke McCullough while handing a debut to Grant and re-calling Williams.
But he kept faith with the 3-5-2 system, using Cedric Evina and Cameron Stewart as wing backs and playing Mitchell Lund and Aaron Taylor-Sinclair either side of Andy Butler.
It was some lovely work from Taylor-Sinclair that created the game's first clear opening, advancing forward and sliding it through for Nathan Tyson whose attempted chip was saved by Jamie Jones.
Colchester responded well and George Moncur twice tested Stuckmann, first with a curling effort after cutting in from the left and then from point-blank range after some hesitant Rovers defending.
The visitors were slightly edging a game being played at a hectic pace and winger Callum Harriott forced another save from Stuckmann, albeit a comfortable one, from distance, while Alex Gilbey blasted a long range effort narrowly wide.
Chances were drying up at both ends as half time approached but Rovers went ahead thanks to a moment of brilliance from Grant. The midfielder picked up possession just outside the area, moved the ball onto his favoured left foot and curled home a sublime effort.
Rovers started the second half in positive fashion. The impressive Tyson saw a low shot from inside the box saved by Jones, before Coppinger might have done better after he latched onto Stewart's through ball but Tosin Olufemi did enough to put him off.
There was a scare for Rovers when Butler sliced a Harriott cross just over.
But within seconds Doncaster doubled their lead from a quick counter, Coppinger leading the charge and squaring for Williams to coolly slot home.
Colchester refused to lie down and Moncur wasted a glorious chance to hit straight back before Stuckmann produced a brilliant stop to claw away Darren Ambrose's close range header.
Substitute Curtis Main should have made it three after good hold-up play from Tyson but after beating two defenders he drilled wide of the far post.
The visitors pressed for a late consolation but Rovers held firm to keep a clean sheet for the first time for two months.
Rovers: Stuckmann, Lund, Butler, Taylor-Sinclair, Evina (Keegan 80), Middleton, Grant, Coppinger, Stewart (McCullough 68), Tyson, Williams. Subs not used: Marosi, Forrester, Wellens, Mandeville.
Colchester: Jones, Olufemi, Elokobi (Kent 64), Eastman, Briggs, Gilbey, Garvan, Harriott, Moncur, Ambrose (Bonne 72), Sordell. Subs not used: Edwards, Lapslie, Sembie-Ferris, Curtis, Parish.