The Spurs full-back was shown a straight red card five minutes from time at White Hart Lane as the hosts went down 2-1 following first-half goals from Bojan and Jonathan Walters.
Nacer Chadli pulled one back for Spurs but Naughton hauled down Victor Moses when the Stoke man was through on goal late on.
As such, Mike Jones showed Naughton a red card and the FA dismissed his subsequent appeal on Tuesday.
"Tottenham Hotspur's Kyle Naughton has had his red card appeal dismissed by an Independent Regulatory Commission hearing," read an FA statement.
"Naughton was dismissed for denying a goal scoring opportunity in the Premier League fixture between Tottenham Hotspur and Stoke City on Sunday 9 November 2014.
"Naughton will serve a two-match suspension with immediate effect as it was his second dismissal of the season."
The 24-year-old defender will now miss Tottenham's Premier League clashes with Hull City and Everton after the international break.
