The 22-year-old forward, who also landed the European Footballer of the Year prize earlier this month, picked up the accolade after collecting four major titles with Barcelona - the Champions League, the Club World Cup, La Liga and the King's Cup.
"This finishes a magnificent year for Barcelona, my team-mates and for me," said Messi after receiving the trophy from UEFA president and former France international Michel Platini.
Portugal and Real Madrid winger Cristiano Ronaldo, last year's winner, was a distant second with 352 points followed by Spain and Barcelona midfielder Xavi (196).
Messi was leading scorer in the 2008-09 Champions League, hitting nine goals including one in the 2-0 final win over Manchester United.
CLUB FORM
Messi's vote appeared to be entirely based on his club form as his performances for Argentina, under coach Diego Maradona, were largely disappointing.
"I don't know," he said. "I try to do the same as I do for Barcelona. But the World Cup qualifiers are complicated, sometimes it's difficult to play and it was a big effort for us to qualify.
"I believe the World Cup could be completely different for us ... it could be better for me and Argentina."
Previous winners:
1991 - Lothar Matthaeus (Germany)
