The image was posted on twitter by Willian, and showed Chelsea's FA Cup celebrations at Wembley, with Conte obscured.
As it was 'World Emoji Day' Willian had covered Conte using the trophy emoji, so that he didn't form part of the photo.
Willian and Conte didn't have a great relationship, and under his management the Brazilian only started 20 Premier League matches.
The tweet was then re-posted by the FA Cup account, and was on the site for at least three hours before it was then taken down.
The FA's caption on the retweet read: "Our #WorldEmojiDay Award for Creativity goes to @willianborges88."
After the tweet was taken down, an FA spokesperson said: "We apologise for any offence caused and we have removed the tweet."
Antonio Conte was fired by Chelsea last Friday, and has now officially been replaced by Maurizio Sarri.