Kenny Miller scored the winner from the spot in the 31st minute after Paul McShane handled Mark Kennedy's corner.
But the Molineux crowd made their feelings clear with chants of "disaster", "Hoddle out" and "sack the board" throughout the game.
Brighton boss Mark McGhee:
"Paul McShane said he got a nudge and that's why he handled it.
"It wasn't a foul but it was enough for him to lose balance and lurch forward which meant his arm went up.
"But I thought we still did enough to win the game because we played better than Wolves, we just didn't take any of the chances we made."
Wolverhampton: Postma (Oakes 45), Lescott, Edwards, Lowe (McNamara 45), Kennedy, Cameron, Miller, Davies, Ross, Aliadiere, Frankowski (Cort 75).
Subs Not Used: Rosa, Seol.
Goals: Miller 31 pen.
Brighton: Henderson, El-Abd, McShane, Lynch, Hinshelwood, Mayo, Nicolas, Frutos (Carole 69), Reid, Noel-Williams, Kazim-Richards (Hart 82).
Subs Not Used: Butters, Loft, Chaigneau.
Ref: N Swarbrick (Lancashire).