MacKenzie volleyed in from close range in the 53rd minute to secure a ninth victory in 11 games for the Dons, who had boss Karl Robinson sent to the stands at half-time for berating referee Carl Berry.
The Dons, who romped to a 5-1 victory at the Weston Homes Community Stadium in November, dominated a low-key first half but an unmarked Luke Chadwick missed their best chance when he headed over Jabo Ibehre’s pin-point cross from only eight yards.
Dean Bowditch drilled two snap-shots narrowly wide and Ibehre fired over from 25 yards, while Colchester striker Steven Gillespie’s free-kick deflected off the Dons wall and just over the crossbar on the stroke of half-time.
The Dons upped the tempo after the break and MacKenzie put them ahead eight minutes after the restart, powering in ahead of U’s defender Magnus Okuonghae to volley home Bowditch’s cross from close range.
Colchester keeper Ben Williams produced good saves to deny Darren Potter, Shaun Williams and Daniel Powell, while Charlie MacDonald clipped a cheeky back-heeled effort inches wide. The U’s piled forward late on in search of an equaliser but Gillespie had a goal ruled out for handball as the Dons hung on.