Substitute Scott Vernon struck the decisive blow three minutes from time to earn the visitors their sixth away win of the season.
It was another bleak result for Brighton, who have now taken just one point from the last 21.
The match started well for Micky Adams' strugglers. Nicky Forster almost put them ahead in the 15th minute with a shot which hit the upright.
The veteran captain only had to wait another six minutes for his eighth goal of the season. Winger Dean Cox jinked inside and crossed for Forster to find the roof of the net with a swivelling header from ten yards.
Colchester offered very little in the first half, but they were gifted a route back into the game with a bizarre own goal in the 35th minute by Brighton defender Adam Hinshelwood.
Hinselwood, making his first home appearance for two years after serious knee problems, was under no pressure when he over-hit a backpass beyond his own keeper John Sullivan.
Brighton had chances to regain the lead after the break. U's keeper Jimmy Walker saved efforts from Glenn Murray and on-loan Leeds midfielder Bradley Johnson.
Clive Platt spurned a good chance to put Colchester ahead midway through the second half when he headed over a cross by Alan Maybury from six yards.
Murray wasted a similar opportunity for Brighton when he headed high and wide from a Matt Richards cross with ten minutes left.
The game seemed to be heading for deadlock but Vernon, brought on in place of Platt, latched on to a pass from Kemal Izzet to claim maximum points for Colchester.