The 22-year-old finished ahead of last year's winner Cristiano Ronaldo by a record 240-point margin, with his Barcelona team mate Xavi in third.
Messi becomes the first Argentine to win the Ballon d'Or, although Argentine-born players Alfredo di Stefano and Omar Sivori, then regarded as Europeans, received the trophy when it was still called the European Footballler of the Year award.
"It's a great honour for me to be voted (as winner of the) Ballon d'Or and to become the first Argentine in history to receive this award," Messi was quoted as saying on the France Football website.
The award caps a brilliant year for the soft-spoken left-footer, who helped treble-winning Barcelona lift the Champions League title with nine goals, as well as bagging 23 in the league and six in the King's Cup.
"I knew I was among the favourites, because Barça have had a prolific year and we won everything, but I didn't expect to win it by such an important margin," Messi added.
The award's 96 jurors gave Messi 473 points out of a possible 480, a near unanimous verdict, the magazine said.
BARCA REWARDED
Portugal's Ronaldo, of Real Madrid picked up 233 points in the vote by journalists from across the world, now open to players from all leagues and nationalities, with Spain's Xavi tallying 170 points.
The jurors rewarded Barcelona's exciting brand of soccer with fourth and fifth place for Andres Iniesta and Samuel Eto'o (now at Inter Milan), respectively.
"The Ballon d'Or is something very important for me," Messi said after his name was added to a list featuring all-time greats such as Johan Cruyff, Franz Beckenbauer, Michel Platini and Zinedine Zidane.
"All those who won it were great players and some great players never won it," added the Argentine, who will receive the award at a ceremony in Paris on Sunday.
Diego Maradona, now the Argentina coach, would probably have won it several times had it been open to non-European players in the 1980s.
The first player from outside Europe to win the Ballon d'Or was Liberia's George Weah in 1995.
Italian and German players have featured prominently in the standings over the years but neither country had a player on this year's 30-strong shortlist.
The other country apart from Spain to have two players in the top 10 was England with Wayne Rooney and Steven Gerrard placing eighth and 10th respectively.
