Barton was dismissed at the Etihad Stadium for an elbow on City striker Carlos Tevez and reacted by then kneeing Sergio Aguero from behind and aiming a head butt at Vincent Kompany.
The governing body has charged Barton and he has until 6pm on Tuesday to respond.
A statement from the governing body read: "The FA has today (Monday 14 May) charged Queens Park Rangers midfielder Joey Barton in relation to two acts of alleged violent conduct during Sunday’s match against Manchester City at the Etihad Stadium.
"Following the player’s dismissal in the 54th minute of the fixture, there followed two incidents involving Manchester City’s Sergio Aguero and Vincent Kompany.
"As Barton had already been dismissed, both of these incidents fell outside of the jurisdiction of the referee.
"Barton has until 6pm on Tuesday 15 May to respond to the charges."
Barton has already incurred a four-match suspension for the initial incident as the dismissal on the final day of the season was his second red card of the season.
Charges of violent conduct, if proven, carry a three-game ban.