Southampton are winless in the Premier League so far this seasonSouthampton manager Ralph Hasenhuttl has been charged by the Football Association over his comments following his side's 3-1 defeat at Chelsea.
The midfielder was initially shown a yellow card by referee Martin Atkinson for a late tackle on Jorginho.
It was upgraded to red after Dean told his colleague to review the challenge on the pitchside monitor.
Austrian Hasenhuttl said he felt "relatively clear" Saints captain Ward-Prowse would be sent off once Dean had instructed Atkinson to review the midfielder's challenge.
Ward-Prowse's dismissal came in the 77th minute at Stamford Bridge with the score at 1-1, before Chelsea struck twice against 10 men to seal victory.
An FA statement read: "It is alleged that comments made by the manager during two post-match interviews constitute improper conduct in that they questioned the integrity of the VAR match official and/or implied bias and/or bring the game into disrepute."
The 54-year-old has until Tuesday, 19 October to respond to the FA charge.
Southampton, who are one of four teams yet to win a Premier League match this season, return to action on Saturday when they host Leeds United.
