The 19-year-old England international, who has recently had his temperament questioned after arguing with David Beckham during England's 1-0 defeat by Northern Ireland on 7 September, will now miss the group games against Benfica and Lille.
Rooney had been initially cautioned by the Danish referee in the 64th minute of the Champions' League game at Villarreal last week, but he received a second yellow card almost immediately for clapping in the official's face.
A Uefa statement said: "Wayne Rooney will miss the club's next two Champions' League matches after his sending-off. The referee considered this [the clapping] dissent and also reported in his post-match report that Rooney swore at him as he left the field."
United could decide to contest the referee's accusation of swearing, but an appeal must be lodged with Uefa officials by midnight on Friday.
Uefa's control and disciplinary body issued a statement which read: "It is beyond any doubt that Wayne Rooney committed several disciplinary offences, notably by taking two yellow cards resulting in a red card, as well as by displaying unsporting conduct. As a result, it is appropriate to impose a two-match ban for the reported misconduct."
The news will not help United's manager, Sir Alex Ferguson, who is without the defender Gabriel Heinze for the rest of the season with a knee injury, while his captain, Roy Keane, is out of action for two months with a broken toe.
Despite concerns over his discipline, Rooney has enjoyed a good start to the season, scoring four goals in all competitions as United have made an unbeaten start to their European and domestic campaigns, in pursuit of Chelsea.
Rooney also collected the FIFPro World Young Player of the Year award at a ceremony in London on Monday. Rooney said: "I love playing football, I enjoy it and I want to win every game. I hope I am here next year."