Barnsley claimed back-to-back wins following their 1-0 victory over Blackpool, and they had Antony Kay to thank for both goals at Layer Road.
Kay scored the fifth and sixth league goals of his short career to secure what was only Barnsley's third win in their last 12 fixtures.
Colchester could not deal with Kay's supremacy in the air at set-pieces, he broke the deadlock in the 34th minute by meeting a corner from Jacob Burns with a delightful backward header which dropped into the net at the far post.
Colchester struggled all night, which was surprising because they had been unbeaten in their previous seven matches, having won their last three.
Yet they never looked like clawing their way back into this game and the match was effectively over when Kay scored his and Barnsley's second in the 55th minute.
Stephen McPhail delivered a free-kick into the box and Kay nipped in front of his marker Richard Garcia to head in beyond keeper Aidan Davison.
The U's then suffered another setback in the first minute of stoppage time when their leading scorer Fagan was sent off for two bookable offences.
Fagan had been booked for a late tackle on Chris Shuker in the 71st minute, and he was then flashed a second yellow and ensuing red card for a clumsy tackle on Burns in injury time.
Fagan will therefore now face a suspension which will cause him to miss Saturday's home game against Hull City.
They rarely threatened to score against Barnsley except for a couple of headers from striker Greg Halford, which didn't really threaten keeper Ross Turnbull.