The former Manchester United manager was sent to the stands for swearing at fourth official James Adcock.
Former Everton and Manchester United manager Moyes was sent to the stands after complaining about a decision by referee Chris Kavanagh not to award a late penalty after Maya Yoshida appeared to trip Victor Anichebe in the box.
Scottish boss Moyes said afterwards he had had been dismissed for swearing at fourth official James Adcock.
"David Moyes has been charged with misconduct by the FA in relation to Sunderland's EFL Cup tie against Southampton," said an FA statement issued Thursday.
"It is alleged that in or around the 90th minute of the fixture Moyes used abusive and/or insulting words towards a match official.
"Moyes has until 6:00pm (1800 GMT) on 1 November 2016 to respond to the charge."
After Wednesday's match, Moyes said: "I was sent off for leaving my box and swearing at the fourth official.
"The problem was he chased me down the touchline. I swore at him and I shouldn't have done so I deserved to be sent off."
Moyes was adamant top-flight basement club Sunderland should have had a penalty against their Premier League rivals, adding: "When you see it again it's a stonewaller, no question.
"Inside the box Yoshida fouls Victor, he comes across him, and it should have been a definite penalty awarded."