Arsenal's new forward Gervinho was sent off on his debut for striking Newcastle's Joey Barton, while their midfielder Alex Song could face sanctions after being charged with violent conduct after stamping on Barton in an incident which was missed by referee Peter Walton.
Both clubs reported the news on their websites and have until August 18 to appeal against the charges.
Arsenal have already said they will appeal Gervinho's sending off.
In a statement the FA said: "Both clubs have been charged following a mass confrontation of players following an incident in which Arsenal's Gervinho was shown a red card in the 75th minute."
There was a mass confrontation of players following the incident with Newcastle's players claiming Gervinho dived to try and gain a penalty.
Following Gervinho's dismissal Arsenal lodged a claim that the standard punishment of a three-match suspension was excessive.
Both clubs have until 16:00 BST on Thursday to respond to the charges. Song must reply by 18:00 BST on Tuesday.
Barton was shown a yellow card for his part in the confrontation.
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