The ban will start immediately, a Football Association spokesman said, meaning the 19-year-old England international misses United's next two league matches against Middlesbrough and Tottenham and their FA Cup tie against Exeter.
Under the FA's new fast-track disciplinary system Rooney had been given until 1800 GMT on Thursday to respond to the charge of violent conduct relating to his clash with Bolton defender Tal Ben Haim on Sunday at Old Trafford.
Rooney pushed Ben Haim in the face during United's 2-0 Premier League win.
Speaking earlier on Thursday, United manager Alex Ferguson launched an angry attack on the FA's new disciplinary system.
Ferguson was annoyed that, unlike under the FA's previous system, the club could not be represented at a disciplinary hearing if the striker denied the charge.
"The system is completely flawed," Ferguson told reporters in Manchester. "The problem for us now is we can't really appeal because we are not allowed to be represented. It is a closed session.
"So therefore they
"As we are approaching 2005, that seems to be unfair and immoral."
Ferguson also said he was bemused by the FA's decision to charge Rooney with violent conduct in the first place.
FERGUSON BEMUSED
Israeli Ben Haim has also been charged with improper conduct for over-reacting. The referee took no action against either player.
"The violent conduct charge bemuses me because every man and his dog would agree it was not violent conduct," Ferguson said.
"If it is violent conduct why are they charging Ben Haim? I can't understand it. He (Ben Haim) is being charged so they therefore believe he is guilty of diving and bringing the game into disrepute."
The FA consulted widely before bringing in its new system this season which is intended to speed up the handling of disciplinary cases.
Rooney will miss Saturday's Premier League trip to Middlesbrough and the home match against Spurs on January 4, together with the FA Cup third round tie against non-league Exeter at Old Trafford on January 8.