Saints' players were furious with referee Mark Clattenburg after he decided Norwich striker Grant Holt had been fouled by Luke Shaw in stoppage time.
Southampton goalkeeper Artur Boruc saved Holt's spot-kick but manager Mauricio Pochettino was also incensed and came on to the pitch to speak to Clattenburg after the final whistle.
Player protests also continued at the end of the game and the club now find themselves in hot water with the authorities.
Southampton have until 4pm on Friday 15 March to respond to the charge.
Southampton is not Manchester United. Pochetino is not Alex Ferguson. With that established, of course Southampton have to be charged. How could anyone expect anything less??- angry bird