After consulting with his assistant, referee Mark Clattenburg ruled that Luke Shaw pushed Grant Holt just inside the penalty area.
Holt missed the subsequent spot-kick with Artur Boruc keeping out his effort, but Southampton players continued to protest after the final whistle, and were joined on the pitch by manager Mauricio Pochettino.
The club has until 4pm on Friday to respond to the charge.
Source: PA
Source: PA