The award has sealed Messi's status as the greatest player of his generation after he saw off Real Madrid rival Cristiano Ronaldo and Barcelona teammate Andres Iniesta for the prize.
Messi received 41.60 percent of votes to 23.68 for Ronaldo, who came second, and 10.91 for Iniesta for the third position.
Messi and former French star, UEFA president Michel Platini, had been the only players to win three straight Ballon d'Or awards, Stuff.co.nz reports.
After winning the honour, Messi said that was incredible to receive the award once again and would like to share it with his Barca teammates.
Spain's Vicente del Bosque was named coach of the year for 2012, seeing off competition from Real Madrid's Jose Mourinho and former Barcelona coach Josep Guardiola, the report added. (ANI )