Anthony Wordsworth's first-half strike gave Colchester all three points and condemned managerless Hartlepool to their eighth consecutive home defeat.
The only goal came when Brian Wilson's floated ball found Wordsworth, who scored at the second attempt after Scott Flinders saved his initial shot.
Karl Duguid and Ian Henderson had already gone close for the visitors.
Hartlepool's best efforts came from James Poole and Antony Sweeney but they could not find a breakthrough.
VIEWS FROM THE DRESSING ROOMS.
Colchester United manager John Ward told BBC Essex:
"It was the proverbial game of two halves. We played very well with some good football in the first period.
"You expect the home team to come back at you which they did.
"We had a fair bit of defending to do, but my goalkeeper didn't have to make the saves he made last week. So it was a really strong performance throughout."