Young has decided not to contest the charge but did query the suspension.
"Ashley Young will be suspended for Manchester United's next three matches," an FA spokesman said.
"He accepted a violent conduct charge following an off-the-ball incident during yesterday's game against Southampton, but argued the suspension was excessive. This was rejected by a regulatory commission."
The 32-year-will miss the New Year's Day match at Everton plus home games with Derby (FA Cup) and Stoke.