The Football Association has charged both clubs with failing to control their players during Chelsea's 3-1 victory at the Etihad on Saturday.
The incident was sparked when Sergio Aguero lunged in on Chelsea defender David Luiz deep into injury time, with players and coaching staff from both teams clashing at the end.
Man City midfielder Fernandinho received a red card and subsequently a three-match ban for grabbing Chelsea midfielder Cesc Fabregas by the throat before pushing him over the advertising hoardings.
Cesc Fabregas will not face any further action over the incident, despite appearing to slap the Brazilian midfielder.
Both clubs have until 18.00 GMT on 8 December to respond to the charge.