But earlier in the game he was involved in an incident with Scott Parker which was not spotted by the match referee.
The 21-year-old has until 6pm on Wednesday to respond to the charge, which relates to an incident in which he appeared to catch Parker's head with his foot during Sunday's 3-2 Barclays Premier League win over Tottenham.
An FA statement read: "The FA has today charged Manchester City forward Mario Balotelli with violent conduct following an incident in his side's home game against Tottenham Hotspur.
"Balotelli was involved in an incident with Tottenham's Scott Parker during Manchester City's 3-2 victory at the Etihad Stadium on Sunday 22 January 2012. Balotelli has until 6pm on Wednesday 25 January 2012 to respond to the charge."
The one consolation for City is that Joleon Lescott will face no further action for catching Younes Kaboul in the face with his forearm in a separate incident at the Etihad Stadium.
If he accepts his charge, Balotelli will miss the Carling Cup semi-final second leg against Liverpool at Anfield. However, should the Italy international decide to appeal he will be free to face the Merseyside giants, with a hearing taking place later this week.
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