Simon Rusk's side found themselves a goal down on the stroke of half-time before Ryan Cooper equalised in the second-half. However the U’s grabbed an all -important second to secure victory.
It was Albion who enjoyed the majority of the early possession and the best of their opening chances fell to Robin Deen who, after seizing on a defensive error, was unable to beat the Colchester keeper one-on-one.
Albion keeper Christian Walton was then forced into an early save once possession had been won by the high-pressing Colchester side, and from the resulting corner the visitors headed just over.
A good low save from the right foot of Walton once again halted the visitors but they took the lead from the resulting corner - the former Plymouth stopper rooted to the spot as the ball was headed past him.
The second half saw Albion begin to reap the rewards for their patient build-up play and a culmination of passes found Elliot Levy with space inside the box, although his effort at goal did little to worry the visiting goalkeeper.
Colchester then rattled Walton’s crossbar at the other end before the Seagulls found their equaliser. A free-kick caused a mix-up between the Colchester keeper and his defender which Cooper capitalised on, bundling the loose ball over the line to make it 1-1.
The goal encouraged the U's to come out and attack but they were consistently frustrated by the organised Albion defence.
The host's best opportunity to go ahead came when Jordan McGuire-Drew unleashed a shot from the edge of the area; however the Colchester keeper was equal to it.
But it was the Essex side who found the telling second goal from another set-piece as a United forward beat Walton to the ball to head home.
It could have been worse for Brighton as a late strike rattled Walton’s crossbar once more before the keeper’s quick reactions denied the U’s on the rebound.
Albion: Walton (GK); Barry, Rea, Cooper, Maguire-Drew; Peake (Asmundsson 65), Wiltshire, Benham; Levy (Muitt 67), Deen, Gray (Rowhurst 80). Suns bot used: Harris, Lall, Horncastle.