Gervinho was sent off in the second half for striking 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: "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 Arsenal's 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, whilst Song must reply by 6pm on 16 August."
Barton received a yellow card for his part in the melee, and as such has already been sanctioned.
Newcastle confirmed in a statement on Monday evening they will deny the charge.
NEXT GAME ... Sat 20th August 2011 - 12.00 ko
SUNDERLAND v NEWCASTLE UTD
PREMIER LEAGUE
NEWCASTLE 0 ARSENAL 0
Krul, Coloccini, Steven Taylor, Ryan Taylor, Simpson, Barton, Cabaye (Lovenkrands 81), Tiote, Gutierrez, Shola Ameobi (Best 73), Ba (Obertan 46).
Subs Not Used: Forster, Williamson, Gosling, Sammy Ameobi.
PRE-SEASON FIXTURES:
NEWCASTLE 0 FIORENTINA 0
(Ab 63 mins)
Krul (Forster 46), Simpson, S Taylor, Coloccini, Enrique, Gosling (Ba 46), Cabaye, Vuckic, Jonas (Marveaux 46) Lovenkrands (R Taylor 61), Best (Shola Ameobi 46).Subs: Sammy Ameobi, Ranger, Tavernier, Williamson.
LEEDS UTD 3 NEWCASTLE 2 (S.Taylor, Vuckic)
Forster, Cabaye, Williamson, Barton, Simpson, Gosling, Gutierrez, Ba, Shola Ameobi, Taylor, Tavernier. Subs: Krul, Taylor, Best, Vuckic, Sammy Ameobi, Dummett.
COLUMBUS CREW 0 NEWCASTLE 3 (Ameobi, Coloccini, Vuckic)
Harper; Tavernier, S Taylor, Coloccini (Dummett, 54), Enrique; Gutierrez (Abeid, 85), Tiote (Smith, 62), Gosling, Marveaux (Vuckic, 76); Ameobi (Best, 75), Ba. Subs not used: Forster, Krul.
ORLANDO CITY 1 NEWCASTLE 0
Forster; R Taylor (Enrique, 26), S Taylor, Coloccini, Tavernier; Gosling (Vuckic, 71), Smith (Abeid, 74), Tiote, Gutierrez; Best (Ba, 74), Lovenkrands (Ameobi, 74). Subs not used: Krul, Harper.
SPORTING KANSAS 0 NEWCASTLE 0
Krul, Gosling, Coloccini, S Taylor, R Taylor, Marveaux (Tavernier 46), Tiote (Abeid 46), Ben Arfa, Gutierrez, Ba (Best 72), Lovenkrands (Smith 46).
DARLINGTON 0 NEWCASTLE 2 (Barton, Sammy Ameobi)
Forster; Simpson (Dummett), S Taylor (Tavernier), Williamson (Henderson), Ferguson (R Taylor); Barton (Abeid), Guthrie (Cabaye, Donaldson), Smith (Gosling), Vuckic (Sammy Ameobi); Ben Arfa (Richardson), Best (Ranger). Subs not used: Soderberg, Newton.