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."
Hartlepool United 01 Flinders 02 Austin 05 Collins 06 Horwood 18 Baldwin Booked 04 Liddle 11 Monkhouse 15 Sweeney 20 Murray (Solano - 73' ) 07 Brown (James - 46' ) 08 Poole (Boyd - 74' ) Substitutes 16 Haslam 03 Humphreys 24 Solano 33 James 10 Boyd Colchester United 01 Williams 03 Rose 04 Okuonghae Booked 06 Heath 20 Wilson Booked 14 Bond 22 Wordsworth Booked 23 James (Izzet - 62' ) 27 Duguid 15 Odejayi 16 Henderson Substitutes 18 Eastman 08 O'Toole 10 Izzet 24 Coker 09 Gillespie