The Yorkshire side were second best for most of this match and they were indebted to an equaliser from super-sub Gary Taylor-Fletcher.
Front runner Taylor-Fletcher appeared as a substitute for the ineffective Pawel Abbott after 57 minutes and he was celebrating his sixth goal of the season just eight minutes later.
The through ball from Tony Carss sprung the offside trap enabling Taylor-Fletcher to burst through and round keeper Aidan Davison. He squeezed the ball home from a narrow angle despite the efforts of George Elokobi on the goalline.
Huddersfield had started the day as joint leaders with Swansea, and while the Welshmen were losing on their way to a draw, they sensed a winner in the later stages.
In fact, the veteran striker Andy Booth rattled the bar late on following a corner from Danny Schofield.
However, it would have been rough justice on Colchester if they had got no reward from this entertaining game.
Elokobi netted the opening goal in the 49th minute after the home side had missed countless chances before the break. Greg Halford flicked on a corner from Kevin Watson and Elokobi steamed in to head home his first ever senior goal.
It was a terrific finish from the 18 year old who was making only his seventh appearance in the first team.
Earlier, United had dominated proceedings and striker Gareth Williams in particular will wonder how he failed to score throughout the afternoon.
Welshman Williams was denied on several occasions by Huddersfield goalkeeper Paul Rachubka and he also struck the woodwork.
Rachubka was possibly Huddersfield's man of the match and he made one great block to thwart Mark Yeates on a one-on-one situation.
When the loose ball broke for Williams, he steadied himself but was unlucky to see his shot cannon back off the post.
Rachubka made further fine saves from the livewire Williams and Tottenham loanee Mark Yeates, but it was not until the second half that Colchester finally got their goal.
This Essex side are now unbeaten in four games but Taylor-Fletcher's equaliser has taken Huddersfield joint top of the pile.