The Football Association have confirmed the defender would face action following a clash with Fulham counterpart Philippe Senderos.
The incident was not seen by the match officials at Craven Cottage - but was caught on video.
Huth has until 6pm on Wednesday to respond to the charge.
Dimitar Berbatov's goal was enough to settle a scrappy contest.
Stoke had been lucky to not be reduced to 10 men midway through the first half after Steven Nzonzi, who had taken a knock on the nose in an earlier collision with Berbatov, was booked for shoving Bryan Ruiz in the face.
Source: PA
Source: PA