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.
The Argentine, who joined Barcelona as a 13-year-old in 2000, claimed 1,073 points in a poll of 147 national team coaches and captains.
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
He also notched the extra-time winner in the 2-1 Club World Cup final victory over Estudiantes in Abu Dhabi on Saturday.
Messi's vote appeared to be entirely based on his club form as his performances for Argentina, under coach Diego Maradona, were largely disappointing.
Argentina struggled to qualify for the World Cup and their results this year included a 6-1 hammering in Bolivia and defeats by Paraguay and Ecuador.
Before the ceremony, Messi told reporters he could not explain why he failed to perform at the same level for his country.
"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."
The FIFA award was introduced in 1991.
Previous winners:
1991 - Lothar Matthaeus (Germany)
1992 - Marco van Basten (Netherlands)
1993 - Roberto Baggio (Italy)
1994 - Romario (Brazil)
1995 - George Weah (Liberia)
1996 - Ronaldo (Brazil)
1997 - Ronaldo
1998 - Zinedine Zidane (France)
1999 - Rivaldo (Brazil)
2000 - Zidane
2001 - Luis Figo (Portugal)
2002 - Ronaldo
2003 - Zidane
2004 - Ronaldinho (Brazil)
2005 - Ronaldinho
2006 - Fabio Cannavaro (Italy)
2007 - Kaka (Brazil)
2008 - Cristiano Ronaldo (Portugal)
