Sir Alex Ferguson was also Messi's selection as the 'Coach of the Year' but most attention will be on the player he omitted.
Of Rooney, Messi told the Uefa website: "I love this type of player. He has a great shot, good control of the ball, uses of his body well in the area. He is a great goalscorer."
The Argentinian genius was similarly fulsome in his praise of United's England centre back.
"He is very good in the air and very strong on his feet," Messi said. "He is very hard to get past."
Messi's team in full was:
Petr Cech (Chelsea), Maicon (Inter), Rio Ferdinand (Manchester United), Carles Puyol (Barcelona), Giovanni van Bronckhorst (Feyenoord), Javier Zanetti (Inter), Xavi (Barcelona), Cesc Fabregas (Arsenal), Andres Iniesta (Barcelona), Sergio Aguero (Atletico Madrid), Wayne Rooney (Manchester United).
After beating Messi for the Ballon d'Or last month, Ronaldo is expected to be named FIFA's World Player of the Year next week ahead of the Argentine.