The charge will come as a shock to Hammers fans who watched their side behave like model professionals in comparison to their fierce London rivals.
West Ham had just one player booked compared to Chelsea's seven.
The Blues also saw Nemanja Matic sent off as well as coach Silvino Louro and manager Jose Mourinho in what has since been described by pundits such as Alan Shearer as an 'embarrassing meltdown', as reported by the Daily Mail.
Hammers in the dock again
Mourinho and his coach Louro have also been hit with misconduct charges.
A statement on the FA's official website confirmed the charges.
"Following the game between West Ham United and Chelsea on Saturday, The FA has taken the following disciplinary action," the statement reads on thefa.com.
"Jose Mourinho has been charged with misconduct in relation to his language and/or behaviour towards the match officials in or around the dressing room area at half-time.
"Chelsea coach Silvino Louro has also been charged with misconduct in relation to his behaviour which led to his 45th minute dismissal from the technical area.
"West Ham have been charged for failing to control their players in the 44th minute of the game and Chelsea have also been charged with the same offence for an alleged breach in the 45th minute of the game.
"All parties have until 6pm on Thursday to reply."
West Ham victim of FA injustice again?
It is the second time this season the Hammers have been charged with the offence after finding themselves in the dock following Mark Noble's dismissal in the 3-0 win at Liverpool back in August.
Skipper Noble, who scored the second goal in his side's historic victory at Anfield, was sent off in the 78th minute when referee Kevin Friend judged him to have fouled Danny Ings.
But even though the decision was reviewed and immediately overturned, the FA still charged the club's players for protesting a decision which even they agreed was wrong.