The FA said in a statement on Thursday that the charges related to the conduct of the players towards referee Mike Dean following the red card shown to midfielder John Obi Mikel after 32 minutes for his lunge on United defender Patrice Evra.
In the statement the FA also named Chelsea assistant coach Steve Clarke and charged him with "using abusive and/or insulting words towards the match officials after the end of the match".
Chelsea and Clarke have until October 12 to respond to the charges.
Chelsea said on their Web site (www.chelseafc.com) that they will defend themselves against the charges.
"Chelsea Football Club will be strongly defending the two charges issued by the Football Association today and will be considering that defence until we have to respond on October 12," the club said in a statement.
Referee Dean reported Chelsea after at least four players surrounded him when he sent off Mikel for the clumsy tackle on Frenchman Evra.
On Tuesday, Mikel lost an appeal against the sending off, and did not play in Wednesday's 4-0 League Cup victory at Championship (second division) side Hull City. He will be suspended for two more matches.
