The former Brighton midfielder curled in a superb set piece from the edge of the penalty area to deny Huddersfield all three points.
Colchester had taken the lead in the 18th minute after Town's Jim Goodwin was penalised for handling Marc Tierney's centre. Hammond made no mistake with the resulting spot-kick.
Huddersfield almost equalised when Gary Roberts took a quick free kick and found Robbie Williams, whose deflected shot was well gathered by Colchester goalkeeper Mark Cousins.
However, six minutes after the restart the hosts were level as Anthony Pilkington tapped home from close range after Cousins had beaten out Lukas Jutkiewicz's fierce left-foot drive.
Huddersfield piled on the pressure and went ahead after 66 minutes when Gary Roberts latched onto Ian Craney's neat pass before thumping his shot beyond Cousins. But they could not hold on and were hit by Hammond's sucker punch.