Town took the lead 11 minutes before half-time through Lee Novak, who planted a low decisive shot past Ben Williams from 20 yards after David Mooney had given away possession.
And the Terriers doubled their advantage three minutes prior to the break when Anthony Pilkington clinically finished from Novak's pass.
Colchester started the second half well and Dave Mooney crashed a 30-yard effort against the crossbar.
But substitute Jordan Rhodes sealed Huddersfield's victory with 11 minutes remaining after polishing off Joe Garner's flick-on.
And although another Terriers substitute Lee Croft was dismissed for two bookable offences with 10 minutes to go, it was all academic.