The Uruguay international had been asked in June by the host of the Canal 10 show for a Spurs player's shirt, to which he replied: "Sonny's? It could be Sonny's cousin too as they all look the same."
British anti-discrimination charity Kick It Out said it had received a "significant number" of complaints related to the comment.
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 in 2020 for using the Spanish term "negrito" (small black person) in a social media post.
