On-loan Wolves defender Danny Batth headed the U's winner just after the hour at the Weston Homes Community Stadium to help them close the gap on second-placed Leeds to a point.
Jason Price hit the woodwork twice for Oldham, who were denied several times by impressive Colchester goalkeeper Ben Williams.
Boothroyd said: "This is our biggest win of the season, for me. It was a tight game. I thought Oldham were really good and we rode our luck at times and so did they.
"We had to make a few changes and everything we did through the week was out of the window, and I thought the lads who came in did very well.
"Everybody pulled together and that's what you need."
Source: Team Talk


