Hartlepool United fell to another away defeat but they stayed outside the relegation zone.
Pools went two down when Kurtis Guthrie headed home in the 63rd minute and then strike partner Chris Porter converted a 78th-minute penalty.
Nathan Thomas's eighth goal of the season eight minutes from time gave Pools hope but the U's held on despite late pressure and nine minutes of injury time.
Pools made a decent start with a couple of early corners, but the first goal threat came from Joe Fryer who saved from Bren Dickenson after a free-kick was whipped into the area/
Further danger followed when Kenton Richardson and Brad Walker lost the ball but Fryer saved smartly from Dickenson at his near post.
Colchester had the ball in net through Porter in the 28th minute but home celebrations ended sharply when the linesman's offside flag was spotted.
Pools were seeing plenty of the ball going forward but the last ball never came off.
Colchester squandered a gilt-edged chance 11 minutes from the interval when a corner from the right came all the way through to the left where the unmarked George Elokobi somehow missed at far post.
Pools continued to play with Nathan Thomas putting over a teasing cross towards Padraig Amond but keeper Sam Walker came out well to gather.
Pools looked in in the 47th minute when Liam Donnelly and Thomas combined down the left, Thomas's early cross looked tailor-made for Amond but ball seemed to rear up and the header went wide.
The away side put their best move together just before the hour, Donnelly, Woods and Amond play ball before Alessandra had his shot blocked.
But when the goal came it was Colchester who got it in the 63rd minute
Pools lost the ball outside their own area and Richard Brindley put in an excellent cross and GUTHRIE could not miss.
However, Pools soon settled back into the game and put together a nice five-man move but Thomas's cross was too close to keeper.
The visiting goal survived more danger in the 73rd minute. A good tackle by Donnelly on Porter seemed to do the trick but Pools could not clear and the U's went just wide in a scramble.
But the game was up when Colchester were awarded a 77th-minute penaltry after clumsy challenge by Donnelly on Guthrie.
Referee Toner pointed to the spot and after yellow-carding Donnelly, PORTER fired in the penalty.
Pools made a double change bringing on Lewis Hawkins and Louis Rooney ffor Oates and Alessandra.
But Pools were back in it in trhe 82nd minute when THOMAS broke into the area and toe-poked the ball low past Walker.
It was an exciting conclusion with home sub Drey Wright bringing a good save from Fryer, diving to his right.
Pools came forward in their numbedrs and Rooney had a shot blocked and Thomas saw an effort deflected for a corner.
Thomas and Featherstone had shots blocked as the boys in pink piled on the pressure.
But despite that and nine minutes of added time, Pools could not find a way through.
HARTLEPOOL UNITED 1
Colchester: Walker, James, Elokobi, Briggs, Brindley (Wright 70), Lapslie, Murray, Garvan, Dickenson, Porter (Fosu 80), Guthrie (Pyke 90)
Subs: Vincent-Young, Wynter, Barnes, Edge
Goals: Guthrie 63, Porter (pen) 78
Booked: Dickenson 29, Wright 85
Pools: Fryer, Richardson, Walker, Harrison, Donnelly, Featherstone, Woods, Alessandra (Hawkins 78), Thomas, Oates (Rooney 78),.Amond
Unused Subs: Dudzinski, Martin, Hawkes, Smith
Goal: Thomas 82
Booked: Woods 57, Donnelly 78
Referee: Ben Toner
Attendance: 3,357 (away 167)