The controversial gesture, which gained notoriety when former West Brom forward Nicolas Anelka used it to celebrate a goal in the club's 3-3 Premier League draw at West Ham in December, is said to have anti-Semitic connotations.
The FA had been investigating the social media postings of the QPR defender - on loan from Tottenham - and the Hull City striker, along with Manchester City's Samir Nasri and Liverpool's Mamadou Sakho.
And the governing body has now opted to take action against Assou-Ekotto and Sagbo for breaches of Rule E3, which relates to players' conduct on social media.
Nasri has been issued a formal warning, while Sakho is "reminded of his responsibilities as a participant".
A statement on Tuesday read: "Having considered the particular facts of each case extremely carefully in consultation with our appointed expert, The FA has today charged Mr Assou-Ekotto and Mr Sagbo with improper conduct contrary to FA Rule E3 in relation to their postings on Twitter.
"It is alleged that in each case the comment was abusive and/or indecent and/or insulting and/or improper, contrary to Rule E3(1).
"It is further alleged that each players' breach of Rule E3(1) was an "Aggravated Breach" as defined in Rule E3(2), as the comment included a reference to ethnic origin and/or race and/or religion or belief.
"Both players have until April 8 2014 to respond to the charges."
Anelka, who insisted his use of the gesture was solely anti-establishment, was handed a five-match ban and an £80,000 fine for his use of the gesture and subsequently left West Brom.
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