Winger Chris Sedgwick and striker Marcus Tudgay returned for the Owls after missing the midweek Carling Cup victory over Bury. Winger Jermaine Johnson was sidelined with a knee problem and midfielder Tommy Miller absent with a calf strain.
The Owls learned before kick-off that they had been drawn at home to Notts County in the Johnstone's Paint Trophy first round.
After the midweek cup victory over Bury, Lewis Buxton, Marcus Tudgay, Chris Sedgwick, Giles Coke, Clinton Morrison and James O'Connor all returned.
After a first half without a goal, Andy Bond opened Colchester's account on 50 minutes.
On-loan Neil Mellor popped up with an equaliser for Wednesday on 83 minutes.
Owls manager Alan Irvine said: "Neil took his goal really well and once he got into that position I expected him to score.
"He's not been firing on all cylinders so far, he's still settling in here, so hopefully that goal will do him a lot of good.
"It certainly gives me plenty to think about regarding my team selection for the next game but it's the kind of problem that managers don't mind having."
Welcome to the Yorkshire Post's exciting match-day service, called Match Centre. Here you will find minute-by-minute updates, stats and team formations. Plus reports from every game in England, from the Premier League down to the Blue Square Premier.
Simply select your game from the pull down menu, then click on the 'i' information button on the right of the fixture and it will give you access to everything you need to know about your team.
So if you can't make it to a game, head for the Match Centre and we will give you the best seat in the house. Click the link below.
For the latest team news, score and commentary from your team check out our new Match Centre