Angry Wednesday fans staged pre-match protests against the Hillsborough board and then chanted 'sack the board' after this dismal defeat.
The loss left Wednesday still flirting with relegation but the points gave Colchester their highest second division points tally.
The deciding goal came from Joe Keith three minutes into the second half when he produced a clever shot from the edge of the box.
Wednesday survived two early scares as the U's came close to snatching the lead on the break.
First Gavin Johnson produced a goal bound header that beat Kevin Pressman, but Derek Geary was on the line to head clear.
And five minutes later the Owls could have gone behind when a cross from Scott McGleish was claimed by Pressman before Geary crashed into him and the ball rolled towards the line, only for Richard Wood to hoof the ball clear.
But Wednesday, who started brightly, had the lion's share of possession and might have found their own way through.
Alan Quinn controlled a 17th minute ball, switched feet and brought a fine save from Simon Brown with his dipping volley.
Youngster Chris Brunt linked with Quinn and then saw his low shot well saved before a looping header from Mark Robins was claimed by Brown.
Brunt showed super skill to skip through two Colchester defenders before firing in a dangerous low ball. It was cleared as far as Wood who spooned his effort over.
And only a last ditch clearance kept out Adam Proudlock as he slid in to connect with a typically clever ball from Robins.
But a bolt from the blue in the 48th minute was enough to give the U's all three points and hand Wednesday their second home league defeat since Christmas.
It came when former West Ham youngster Keith hit a dipping shot that caught Pressman slightly off his line and crept under the bar.