The English Football Association said on its official website that Israeli Ben Haim had also been charged with improper conduct over the incident.
Television pictures showed 19-year-old England international Rooney pushing his hand into Ben Haim's face in the first half of United's 2-0 win, although the incident was missed by the referee.
United manager Alex Ferguson later criticised Ben Haim, claiming he over-reacted by falling to the ground in apparent agony after the incident.
Under the FA's new disciplinary system Rooney has until 1700 GMT on Thursday to respond to the charge.
If he accepts he was at fault he will be banned immediately for three matches. Otherwise a disciplinary hearing will examine the case on Friday.
Ben Haim has until January 20 to respond to his charge as improper conduct is not covered by the FA's fast-track system.
