But German keeper Heinz Muller enhanced his own hero status at Oakwell with two second-half saves despite being crippled by a first-half injury.
The goal took Macken's tally to an impressive four goals in three matches for the Oakwell side - separated by his two-month spell back at Pride Park.
His first goals came in a loan spell at the end of last year, but after an eight match league run without a win he was the perfect tonic for Barnsley.
The home side suffered a huge setback midway through the first half when the game was stopped for five minutes when Muller was floored with a knee injury.
The Tykes did not have a replacement keeper on the bench and it was touch and go whether he would continue, but he hobbled on and managed to block a 25 yarder from Phil Ifil with the injured knee.
Then Macken gave Barnsley the lead on the stroke of half-time when he finished off from ten yards after Danny Nardiello's header was blocked by Chris Coyne.
But then it was Muller's turn to hog the limelight and only a brave save early in the second half denied Colchester when Kevin Lisbie squeezed through the defence and then another super stop denied Johnnie Jackson.
Afterwards Colchester boss Geraint Williams said: "I felt at the start we were positive, got two or three very good chances and we were caught with a sucker punch.
"I don't think Dean Gerken had another save to make apart from picking ball out of the net.
"I don't know how serious the keeper's injury was but he made some great saves and we didn't put him under enough pressure..
"It leaves us at the bottom and it is going to be difficult to get out of it. We have got to pick up wins and probably average a point-and-a-half from every game."