Gunners forward Gervinho was sent off in the second half for striking Newcastle midfielder Joey Barton after the pair had squared up following what the home side claimed was a dive in the penalty area.
Arsenal have appealed that red card, but their midfielder Alex Song could now also face disciplinary action after his stamp on Barton, which had inflamed the situation, was missed by referee Peter Walton.
A statement from the FA read: "Newcastle United and Arsenal have been charged by The FA with failing to control their players following Saturday's (13 August) fixture at St James' Park.
"Both clubs have been charged following a mass confrontation of players following an incident in which Arsenals Gervinho was also shown a red card in the 75th minute.
"Following Gervinho's dismissal Arsenal have today lodged a claim that the standard punishment of a three-match suspension is clearly excessive. A Regulatory Commission will hear the claim on 16 August."
Meanwhile, Arsenal's Alex Song has been charged separately by The FA with violent conduct following an incident earlier in the same fixture.
Both clubs have until 4pm on 18 August to respond to the charge, while Song must reply by 6pm on 16 August.
As it stands, Gervinho would serve an automatic three-match ban - missing games against Liverpool and Manchester United - and Song could also be hit by the same retrospective punishment.
Barton, meanwhile, received a yellow card for his part in the melee, and as such has already been sanctioned.
The controversial midfielder admitted he went down easily following Gervinhos slap, and also engaged in some heated exchanges on Twitter, a social media platform which the FA continue to keep a close eye on.
Newcastle confirmed in a statement this evening they will deny the charge.