Craig Eastmond's 72nd minute strike was all that separated two average sides both embroiled in a mid season relegation scrap. Neither side had too many chances but Tom Eaves and Simon Gillett came closest for a Glovers side that huffed and puffed but proved toothless in front of goal.
The defeat dropped Yeovil down to 22nd place in the table, falling behind today's opponents who just about deserved their victory with ex-Yeovil loanee Gavin Massey impressing at left midfield.
Yeovil made one change to the side that beat Accrington 2-0 in the second round replay of the FA Cup on Tuesday night. Up front, Sam Hoskins came in for James Hayter while Cup goalscorer Kieffer Moore missed out completely with an ankle injury.
The first half was forgettable; in fact, the first twenty minutes saw only a half chance for either side but Massey then went close after cutting inside and firing at Jed Steer. Yeovil's best chance fell to Simon Gillett who chested a Sam Foley ball down before forcing Sam Walker into a fine save with his volley.
The second half couldn't be worse and it actually started at a better tempo with Steven Arthurworrey flicking over and Foley testing Walker with a shot that the former Yeovil keeper pushed over the top. It sparked Colchester into action and Freddie Sears shot at Steer after some good build up play.
Tom Eaves volleyed way over from a Nathan Smith throw in and Sam Hoskins sliced a shot well wide before manager Gary Johnson made a double change on the hour mark. Brendon Moloney and Hoskins came off with Ajay Leitch-Smith and James Hayter replacing them.
After Eaves had a header caught by Walker, the U's took the lead on 72 minutes when after a good move involving Massey down the left, the ball was swept in with his left foot by Craig Eastmond.
Yeovil's chance count was barely increasing despite having plenty of possession. Joe Edwards volleyed wide from Hayter's chest down and then Eaves headed straight at Walker late on as Yeovil pushed Ryan Inniss on as a sub up front as they tried desperately to grab something from the game.