The club have been charged with failing to ensure their players conducted themselves in an orderly fashion after referee Martin Atkinson awarded Villa a late penalty for an alleged foul by Roger Johnson on Gabriel Agbonlahor.
Right-back Stephen Carr has been charged with improper conduct for gesturing towards the home fans at the end of the match and centre-back Johnson has been asked to explain his comments to the media about the referee after Blues' 1-0 defeat at Villa Park on Sunday.
"Birmingham City FC have been charged with failing to ensure their players conducted themselves in an orderly fashion, relating to the players' behaviour towards referee Martin Atkinson following the awarding of a spot-kick to Aston Villa late in the fixture," an FA statement read.
"Birmingham City defender Stephen Carr has been charged with improper conduct following an incident at the end of the same fixture.
"Meanwhile Roger Johnson, also of City, has been asked to explain comments made to the media after the fixture in relation to referee Martin Atkinson."