The incident in question occurred when Rovers striker Morten Gamst Pedersen challenged Chelsea goalkeeper Petr Cech and players from both sides became involved in a scuffle..
Blues midfielder Claude Makelele became involved and was followed by a number of other players on both sides.
An FA statement said: "The charges relate to a mass confrontation during the Premier League match at Ewood Park on Wednesday, 2 February.
"The two clubs have until Monday, 21st February to respond to the charges."