The 20-year-old, voted the PFA Young Player of the Year last weekend after a sensational first season in the top flight, was caught on video deliberately swinging his arm into the stomach of West Bromwich Albion's Claudio Yacob during Monday's 1-1 draw at White Hart Lane.
Because the incident was not seen by the match referee it was referred to the FA's Independent Regulatory Commission who on Thursday retrospectively found him guilty of the charge.
Alli had not disputed the charge but contested that the automatic three-match ban for such incidents would be 'clearly excessive' the FA said in a statement.
His absence will be a further blow to Tottenham's hopes of winning their first English league title since 1961.
He has scored 10 league goals this season with nine assists and will be part of England's European Championship squad.
Tottenham's draw against West Brom left them seven points behind leaders Leicester City with three matches left, beginning with the trip to London rivals Chelsea on Monday.
Leicester can clinch the title if they beat Manchester United on Sunday.
(Reporting by Martyn Herman, editing by Pritha Sarkar)
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