Ward-Prowse thought he had opened the scoring at St Mary’s Stadium when his 63rd minute shot was deflected in, only for the effort to be ruled out for a foul on Jacob Ramey in the build-up following a VAR check.
Villa’s players were furious the goal was initially rewarded, with midfielder Douglas Luiz booked by referee Michael Salisbury, prior to the official overturning his original decision.
The FA has decided the complaints exceeded acceptable levels and charged the club with failing to ensure players conducted themselves in an orderly fashion. Villa have until Friday to respond to the charge.
An FA statement read: “Aston Villa has been charged with breaching FA Rule E20 during its Premier League game against Southampton.
“It is alleged Aston Villa failed to ensure its players conducted themselves in an orderly fashion during the 65th minute.”