The FA charged the Premier League club after the players surrounded referee Michael Oliver after he showed Lewis-Skelly a straight red card for a foul on Matt Doherty on January 25th.
"An independent Regulatory Commission has imposed a £65,000 fine on Arsenal... (as) it was alleged that Arsenal failed to ensure their players did not behave in an improper way around the 43rd minute, and the club subsequently admitted to this charge," the FA said in a statement.
The video assistant referee (VAR) upheld Oliver's decision at the time of the incident but Arsenal subsequently appealed against the red card and his three-match ban was overturned.
The FA's statement included a letter from Arsenal, who highlighted that the players "did not behave in a way which was offensive, violent, threatening, abusive, indecent, insulting or provocative."
But the FA responded by saying that "there were, at times, nine AFC players in very close proximity to the referee" and that the red card "being overturned on appeal does not justify the reaction and affords no mitigation."