The Football Association has said the Gunners will have until Tuesday to respond.
The charge relates to an incident in the fifth minute of stoppage time when a number of Arsenal players surrounded referee Andrew Madley to claim a penalty for a possible handball.
Madley, who issued nine yellow cards in what became a fractious and scrappy encounter at the Emirates Stadium, dismissed their appeals.
An FA statement read: "Arsenal FC have been charged with a breach of FA rule E20.1 following their Premier League match against Newcastle United FC on Tuesday, January 3 2023.
"It is alleged that Arsenal FC failed to ensure their players conducted themselves in an orderly fashion in the 95th minute, and the club have until Tuesday, January 10 2023 to respond."