Hemed scored the winner in Brighton's 1-0 league victory over Newcastle on Sunday but was involved in an incident with Magpies defender Yedlin in the 88th minute.
An FA statement read: "Tomer Hemed has been charged for an alleged act of violent conduct which was not seen by the match officials but caught on video.
"He has until 6pm on Tuesday [26 September 2017] to respond to the charge."
Brighton manager Chris Hughton came to the Israel international's defence after the game, insisting that the striker's stamp on Yedlin was an accident.
"I have seen it, and my absolute impression was that there was no intention, particularly knowing the player," said Hughton.
"My first impression was that there was absolutely no intent. I was unaware of it at the time, and I have just been shown it."