Saints players surrounded referee Mark Clattenburg after he awarded a penalty for a foul by Luke Shaw on Grant Holt in injury time. Artur Boruc saved Holt's subsequent penalty, and the game ended level.
It is not the first incident that Clattenburg has been involved in this season, as he was at the center of a controversy earlier in the campaign involving claims from Chelsea players that he racially abused John Obi Mikel before being cleared of the allegations.
On Friday, the FA confirmed that Southampton admitted to a charge of failing to control its players and had issued the fine as a result. Southampton has won just one of the seven matches it has played under new boss Mauricio Pochettino and sits 16th in the Premier League table as it attempts to stave off relegation.