The 29-year-old striker will miss matches against Everton, West Ham and Middlesbrough.
The 29-year-old, who had returned to form with a hat-trick against Manchester City in the previous game, will miss matches against Everton, West Ham and Middlesbrough.
The FA rejected the club's claim of wrongful dismissal, which hinged upon Vardy being off-balance as he was harried by Glen Johnson when he challenged Stoke midfielder Mame Diouf just before the half-hour mark.
Referee Craig Pawson did not hesitate in showing him a red card for the two-footed challenge.
"Jamie Vardy will serve a three-match suspension with immediate effect after his wrongful dismissal claim was rejected, following an Independent Regulatory Commission hearing," read the FA statement.
"The Leicester City striker was sent off for serious foul play during the game at Stoke City on Saturday 17 December 2016."
Vardy's suspension means Leicester will be without three key players for the game with Everton next Monday.
Defenders Christian Fuchs and Robert Huth will be absent as they serve a one-match suspension for picking up their fifth bookings of the campaign in Saturday's ill-tempered Stoke match.
They were two of five Leicester players to be booked by Pawson in the final seven minutes of the first half -- leading to angry scenes at the break -- in a match which saw them come from 2-0 down to secure a 2-2 draw.
Pawson had been criticised for not sending off Manchester United defender Marcos Rojo for a similar two-footed challenge in their Premier League clash with Crystal Palace only a few days prior to the Vardy incident.
Leicester currently sit a lowly 15th in the table, just three points clear of the relegation places.