The visitors had looked dead and buried after 18 minutes but a goal in first-half stoppage time changed the complexion of the match.
Colchester were a different team after the break and a close-range volley from Chris Iwelumo kept them on course for automatic promotion.
Chesterfield thoroughly deserved to halt a run of five successive home defeats after they played some of their best football in weeks in the first period.
Jamie O'Hara scored a brilliant third-minute opener from 25 yards and Paul Hall tucked away a penalty after Alex Bailey was pulled down by Karl Duguid.
The referee at first did not award a spot-kick but the linesman clearly signalled a foul and Hall sent Aidan Davison the wrong way as he slipped the ball into the bottom right-hand corner.
Colchester gave themselves hope in the third minute of stoppage time when Mark Yeates went past three defenders before sliding a shot under Barry Roche and in off the far post and the second period was a different story.
Tony Thorpe should have equalised in the 57th minute but headed wide from eight yards and Colchester always threatened to draw level as Neil Danns started to dominate the midfield.
The equaliser came when Duguid found space on the left to cross for Iwelumo to volley into the top left corner from six yards.
Both teams could have won it in a frantic last 15 minutes with O'Hara striking the inside of a post with another long-range effort.
Danns also had a shot charged down and the midfielder was only denied by a well-timed tackle as he prepared to shoot right at the end.
But a draw was a fair result and it leaves the race for second place wide open.