Argentine Messi was also named forward of the year with his club mate Xavi Hernandez, who also played a key role for Barca last season, named as midfielder of the year ahead of a third Barcelona club mate Andres Iniesta.
Chelsea and England skipper John Terry was named defender of the year while Edwin Van der Sar, of last season's Champions League runners-up Manchester United, was named goalkeeper of the year.
Thee awards are for their performances in the Champions League.
UEFA president Michel Platini presented a special award to Paolo Maldini, who won five European Cups with AC Milan during a playing career that spanned more than 20 years until he retired at the end of last season.