The charge relates to an incident in the second half of the Premier League clash when Villa striker Christian Benteke was shown a straight red card.
Belgium international Benteke was dismissed for raising his hand in Ryan Mason's face after the Tottenham midfielder had squared up to him off the ball.
Tempers flared following that altercation, with players from both sides having to be separated, and the FA on Wednesday revealed that the two clubs have been charged for their conduct.
"Both Aston Villa and Tottenham Hotspur have been charged by The FA following their game on Sunday 2 November 2014," said a statement on the FA's official website.
"It is alleged that in or around the 66th minute of the game, the clubs failed to ensure their players conducted themselves in an orderly fashion.
"Both clubs have until 6pm on 10 November 2014 to respond to the charge."
Benteke was handed a three-match ban for his sending off.
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