The misconduct was not seen by the match officials at the time but was caught on video by the FA, who reviewed the incident on Monday.
Deeney will miss Watford's next three league games against Everton (Nov. 5), West Ham United (Nov. 19) and Newcastle United (Nov. 25).
Watford and Stoke City have also been charged by the FA for failing to control their players during the match.
Both clubs have until 1800 GMT on Friday to respond to the charge.
(Reporting by Hardik Vyas in Bengaluru, editing by Ed Osmond and Christian Radnedge)
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