The FA also rejected the two clubs' appeals for false dismissals of players Emmanuel Adebayor and John Obi Mikel.
African trio Kolo Toure, Emmanuel Adebayor(Arsenal) and John Obi Mikel (Chelsea) were all shown red after the mass brawl that erupted late in the Carling Cup final.
Toure, who did not make an appeal, will automatically serve a three-match ban as well as his teammate Adebayor who had his appeal rejected.
The Togolese forward could be hit with a further sanction as he was charged for 'reacting aggressively and failing to leave the field of play immediately'.
Nigerian John Obi Mikel will be out for four games as the sending off is his second of the season.
Another African defender, Arsenal right-back Emmanuel Eboue, has been also charged with violent conduct after striking Chelsea defender Wayne Bridge even though the Ivorian was not cautioned after the incident.
A statement from the FA read "Arsenal and Chelsea have been charged with misconduct for an incident involving players and officials from both clubs towards the end of the Carling Cup final on Sunday, February 25.
"Arsenal's Emmanuel Eboue has been charged with violent conduct for striking Chelsea's Wayne Bridge. He has until 6pm tomorrow to respond, and the case will be heard by a disciplinary commission on Thursday on the basis of documents and video evidence.
"Emmanuel Adebayor has been charged with reacting aggressively and failing to leave the field of play immediately after being sent off. He has until 6pm tomorrow to respond to the charge and his case will be heard by a disciplinary commission on Tuesday, March 6." The statement added.