The Evo-Stik Premier League outfit battled valiantly to bridge the 113-place chasm with their opponents.
But after goals from Francisco Sandaza and Inigo Calderon had given the visitors a two-goal cushion at the break, FC United’s comeback dreams were ended when Jake Cottrell missed a penalty midway through the second period.
Elliott Bennett and Matt Sparrow sealed a victory that earned Brighton a south coast derby with last season’s finalists Portsmouth.
For FC United, there was the consolation of what appeared to be a record crowd, in excess of 7,000 bringing in useful revenue ahead of their proposed new ground move.
FC UNITED OF MANCHESTER: Ashton, Jacobs (Battersby 81), Munroe, Platt, Quistin (Carden 90), Roca, Parker, Cotterill, Ovington (Wolfenden 59), Mike Norton, Deegan.
BRIGHTON: Brezovan, Calderon, Greer, El-Abd, Painter, Bridcutt, Kishishev (Smith 75), Bennett (Baz 89), Sparrow, Sandaza, Murray (Hart 72).
Ref: Eddie Ilderton (Tyne & Wear).