Argentina star Messi was selected ahead of Barcelona team-mates Xavi and Andres Iniesta, who both won the World Cup with Spain last summer.
Messi, 23, scored an astonishing 60 goals for club and country in 2010 and is regarded by many as the most gifted player of his generation.
The FIFA Ballon d'Or was created following the merging of France Football magazine's European Footballer of the Year prize with the FIFA World Player of the Year gong.
As such, it is awarded based on votes cast by journalists from around the world and coaches and captains of national teams.
Messi was the holder of both titles and therefore joins former Brazil strikers Ronaldo and Rivaldo and France legend Zinedine Zidane as a multiple winner of the latter accolade.
Alfredo Di Stefano, Johan Cruyff, Franz Beckenbauer, Kevin Keegan, Michel Platini, Marco van Basten, Karl-Heinz Rummenigge and Ronaldo are the only other men to win the Ballon d'Or more than once.
Messi also became the first player to be awarded the prize in a World Cup year without having won the tournament for the first time since 1994 (when non-Europeans were ineligible).
Jose Mourinho was named Coach of the Year ahead of World Cup-winning Spain boss Vicente del Bosque and Barcelona's Pep Guardiola for leading Inter Milan to an unprecedented Champions League, Serie A and Coppa Italia treble.
There was disappointment for Glentoran's Matty Burrows in the Goal of the Year prize, with his jaw-dropping backheeled volley against Portadown losing out to Hamit Altintop's relatively mundane volley for Turkey against Kazakhstan.
Meanwhile, tearful Brazil great Marta won a record fifth successive Women's Player of the Year award.
Team of the Year
Goalkeeper: Iker Casillas (Real Madrid and Spain);
Defenders: Maicon (Inter Milan and Brazil), Gerard Pique (Barcelona and Spain), Lucio (Inter Milan and Brazil), Carles Puyol (Barcelona and Spain);
Midfielders: Andres Iniesta (Barcelona and Spain), Xavi (Barcelona and Spain), Wesley Sneijder (Inter Milan and Holland);
Forwards: Cristiano Ronaldo (Real Madrid and Portugal), David Villa (Barcelona and Spain), Lionel Messi (Barcelona and Argentina).
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