The France international took to Instagram after City's 2-1 win over Burnley on January 2, which saw Pep Guardiola's side come from behind and a man down to claim all three points.
Sagna's comment appeared to be aimed at referee Lee Mason, who showed Fernandinho a straight red card for his two-footed challenge on Johann Berg Gudmundsson in the 32nd minute.
The 33-year-old right-back wrote on the social media platform: "10 against 12... but still fighting and winning as a team" which he later doctored to read: "still fighting and winning as a team."
Sagna has now been charged by the FA, who issued a statement which read: "It is alleged that a comment posted on social media by the Manchester City defender constituted improper conduct in that it questioned the integrity of the match official and/or alleged and/or implied bias on the part of the match official, and/or brought the game into disrepute.
"He has until 6pm on 13 January 2017 to respond to the charge."