The German centre-back, who will also pay a £15,000 fine and attend an educational course, responded to tweets sent from an account which posts sexual images and invites users to guess the gender of individuals in the pictures.
Huth deleted the tweets and later issued an apology for any offence caused by his actions.
He tweeted: "Clearly no offence was meant or directed to anyone, but apologies if I've offended anyone."
However, Huth will now serve a suspension after the former Chelsea man admitted a charge over his use of social media.
A statement on the governing body's official website said: "Robert Huth will serve a two-match suspension with immediate effect after he admitted breaching FA Rules in relation to comments he made on social media,
"The Stoke City defender was charged in relation to comments which were indecent and/or improper and/or brought the game into disrepute, contrary to FA Rule E3(1).
"Further to this, it was considered an 'Aggravated Breach' as defined in Rule E3(2), as it included a reference to gender and/or gender reassignment.
"Huth was also fined £15,000 and ordered to complete a mandatory education course."
The news comes on the same day Stoke boss Mark Hughes appeared to open the door for Huth to join Leicester City on loan.
"Robert indicated that he wanted to play and the likelihood of him playing here in the coming weeks was probably low," he said. "We both agreed that he needed games so it is an opportunity for him.
"We would probably have preferred a Championship club because we would have had a recall clause, but it's a good opportunity for him to get back to playing some Premier League football."
