First-half goals from Neal Bishop and Alan Judge proved enough to give the Magpies victory.
The U's pushed hard to get back in the game in the second half and Ian Henderson's effort clipped the bar, while Magnus Okuonghae had a shot tipped over the bar by Notts County goalkeeper Bartosz Bialkowski.
But they could not find a goal and suffered their first home defeat under boss Joe Dunne.
It was also the first time that Colchester had failed to score since Dunne took over at the end of September.
For a full match report and pictures from the U's defeat against Notts County, see Wednesday's Daily Gazette.