The Uruguay international had been requested a Spurs player's shirt by the host of the Canal 10 show in June. His response was: "Sonny's? It could also be Sonny's cousin, they all have a similar look."
British anti-discrimination charity Kick It Out said it had received a "significant number" of complaints related to the comment.
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Bentancur apologised to the South Korea international and Spurs skipper, who said his team-mate had "made a mistake".
A statement from the FA said Bentancur had been charged with an alleged breach of its rules in relation to a media interview.
"It's alleged that the Tottenham midfielder has breached FA Rule E3.1 as he acted in an improper manner and/or used abusive and/or insulting words and/or brought the game into disrepute," the statement said.
"It's further alleged that this constitutes an 'aggravated breach' which is defined in FA Rule E3.2, as it included a reference, whether express or implied, to nationality and/or race and/or ethnic origin."
Bentancur has until September 19 to provide a response to the charge.
Former Manchester United striker Edinson Cavani was banned for three games and fined £100,000 ($130,000) in 2020 for using the Spanish term "negrito" (small black person) in a social media post.
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