Owusu, on loan from Cheltenham, headed in Gary Borrowdale's free-kick 11 minutes into the second half to score his 12th goal of the season and clinch the Seagulls a precious victory.
Brighton goalkeeper Michel Kuipers denied Colchester duo Mark Yeates and Ashley Vincent in a forgettable first half but the Seagulls also threatened.
Former U's defender Adam Virgo's weak shot was saved easily by Colchester goalkeeper Dean Gerken from close range, and Tommy Elphick headed over from Dean Cox's corner.
The Seagulls started the second half brightly and broke the deadlock in the 57th minute when Owusu powerfully headed in Borrowdale's free-kick after Chris Coyne had fouled Gary Hart.
And Brighton substitute Craig Davies almost capped their vital victory with five minutes to go, only to be denied by Gerken.