Huth caught Fulham defender Philippe Senderos in the face with his arm during Saturday's Premier League at Craven Cottage and, although the incident was not spotted by the match officials, it did appear in video footage.
The FA subsequently confirmed that Huth would face a violent conduct charge and that he would have until 6pm on Wednesday to respond, although the club were given an additional 24 hours to consider their response.
A statement on Stoke's official website read: "Robert Huth has accepted the charge of violent conduct following an incident in last weekend's game.
"The German international will now have to serve a three-match suspension, which means he will miss the West Ham, Newcastle and West Brom games."
Stoke may have been mindful of the fact that an extra match can be added to bans if any appeal is judged to be frivolous.
Huth has been teaming up with Ryan Shawcross at the heart of the Stoke defence and Tony Pulis must now decide who should deputise for him.
Versatile United States international Geoff Cameron may be the leading candidate but full-backs Ryan Shotton and Marc Wilson could also be in the frame.