Messi was on a three-man shortlist with Barca team-mates Xavi and Andres Iniesta but, despite Spain's World Cup triumph, the Argentina forward came out on top in the voting.
He becomes the first winner of the FIFA Ballon d'Or, which merges France Football magazine's European Footballer of the Year prize with the FIFA World Player of the Year. The awards were based on the votes of the coaches and captains of national sides as well as global journalists.
Messi scored more than any other player in Europe's top five leagues in 2010, with 42 goals in 36 La Liga games, as well as finishing top scorer in the Champions League in 2010 with 12 goals in 12 games.
He totalled 60 goals for the year for club and country.
"To be honest, I didn't expect to win today, but it was already great to be here next to my two mates," Messi said as he accepted the award. "To win it makes it even more special.
"I want to share with all of my friends, my family, all the Barcelonistas and the Argentinians."
Real Madrid coach Jose Mourinho had earlier been named FIFA World Coach of the Year for Men's Football. Mourinho won Serie A, the Champions League and Coppa Italia with Inter Milan in the 2009-10 season and has made an impressive start to life at the Bernabeu.
In his acceptance speech, Mourinho paid tribute to Spain's Vicente Del Bosque and Barcelona's Pep Guardiola, who had been shortlisted for the award.
Speaking to Sky Sport Italia, he also reserved special praise for the players and staff at Inter.
"I'm the best coach in the world for 2010 because I was the coach of the best team in the world in 2010," he said. "We were a family and we continue to be a family. I continue to be part of it from afar.
"I want Inter to win every game except those against my team."
Hamit Altintop won the FIFA Puskas Award for best goal in recognition of his strike for Turkey against Kazakhstan.
FIFA Men's World Player of the Year: Lionel Messi
FIFA Women's World Player of the Year: Marta
FIFA World Coach of the Year for Men's Football: Jose Mourinho
FIFA World Coach of the Year for Women's Football: Silvia Neid
FIFA FIFPro World XI of 2010: Iker Casillas; Maicon, Gerard Pique, Lucio, Carles Puyol; Xavi Hernandez, Wesley Sneijder, Andres Iniesta; Cristiano Ronaldo, David Villa, Lionel Messi
FIFA Puskas Award: Hamit Altintop
FIFA Fair Play Award: Haiti Under-17 women's team
FIFA Presidential Award: Archbishop Desmond Tutu
