The Italian tangled with Spurs' Scott Parker in the second half at the Etihad Stadium, appearing to stamp on the head of the England midfielder.
Having already been sent off against Liverpool in November, Balotelli faces a four-game ban if he accepts the charge.
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 has until 6pm on Wednesday 25 January 2012 to respond to the charge."
Referee Howard Webb acknowledged the incident had occurred during the weekend clash but refused to discipline Balotelli, who had already been booked after replacing Edin Dzeko.
Webb, who took charge of the 2010 World Cup final, will have been obligated to mention the fracas in his post-match report, but having rejected the opportunity to punish the offence during the game, The FA are only permitted to take retrospective action if the official deems he didn't take the necessary action.
After escaping being penalised, Balotelli swept home the winner from the penalty spot in stoppage time, following Ledley King's foul on the effervescent forward, to maintain City's three-point lead at the top of the Barclays Premier League.
Tottenham boss Harry Redknapp launched a scathing attack on Balotelli after the game and called on The FA take action against the City forward.
"I'm sure they [FA] will look at it," Redknapp said. "They must do, mustn't they? It's not the first time he's done that is it and I'm sure it won't be the last.
"The first [stamp] could be an accident, but the second one? He's back-heeled him straight in the head. I don't like talking about people kicking players in the head, but when you see that, it's wrong. It's blatantly obvious.
"Whether he gets sent off or whatever, it's wrong and I don't like seeing people react like that to a challenge.
"Scott made a good block. He [Balotelli] reacts like that at times to challenges, but Scott now has a lovely cut on his head. I don't see any reason. What reason did he have to kick Scott in the head with his studs while he is lying on the floor?
"It's not something I understand. How you can back-heel somebody in the head when they are lying on the floor? "It's not a nice thing to do and it has no place in football."
With captain Vincent Kompany still serving his four-game ban following his sending off against Manchester United in the FA Cup, and Ivory Coast internationals Kolo and Yaya Toure currently away on Africa Cup of Nations duty, Roberto Mancini faces losing another of his star turns on the eve on the Carling Cup semi-final second leg against Liverpool at Anfield.
However, Balotelli, who has picked up 17 yellow cards and three red in his 18-month City career, is in danger of having his ban extended should any subsequent appeal be deemed frivolous.
If City opt against an appeal, Balotelli will miss the tie with Liverpool, as well as the Premier League trip to Everton, the home game with Fulham and the visit to Aston Villa.
An option to appeal would delay the ban, leaving him eligible to feature against The Reds on Wednesday, but potentially see his absence extended if upheld, which is likely see him miss the Carling Cup final at Wembley.
Having netted 12 goals this season, Balotelli has often proved himself to be an able match-winner in City's ranks, however, arguments with manager Mancini, as well as fellow teammates, have often worked to undermine his tenure in the Premier League.