The Seagulls players were angry with referee Peter Walton's decision to award Southampton a penalty for Lewis Dunk's challenge on Jose Fonte, which replays showed had occurred outside the area.
Mauricio Taricco, Albion's player/assistant manager, was sent off for dissent as he led the protests and the 10 men went on to lose the match 3-0.
An FA statement read: "Brighton and Hove Albion have been fined £15,000 and severely censured for failing to ensure its players conducted themselves in an orderly fashion.
"The incident occurred during the club's match at Southampton on 19 November 2011. Brighton had denied the charge and requested a personal hearing."