The Belgian clashed with the England international on many occasions during the 1-1 draw between the sides on Saturday, and the FA has confirmed that the midfielder has been charged with violent conduct.
Referee Mark Halsey confirmed that he had not seen the incident in the 59th minute, when Fellaini headbutted his opponent, but stated that he saw other incidents where the midfielder appeared to elbow Shawcross in the 71st minute before pushing him in the face in the 91st minute and deemed neither to be violent conduct.
The player had until Tuesday evening to respond, but both Everton and Fellaini have already accepted the charge, and he will now miss the away game at West Ham and the home matches against Wigan and Chelsea, ruling him out until the fixture against Newcastle on New Year's Day.
"I apologize completely to Ryan Shawcross, my teammates and to our fans at the game," Fellaini said. "There was a lot of pushing and pulling going on inside the Stoke penalty area and I didn't feel I was getting any protection from the officials. Nevertheless I know I shouldn't have done what I did.
"I have also apologized to the manager and the staff. I have no excuses, I was disappointed with the way I was being treated and I lost my temper, which was unprofessional of me."