The Argentina international went one better than his runner-up placing in both 2007 and 2008 and managed to turn the tables on former Manchester United and current Real Madrid winger Cristiano Ronaldo who beat him to the title last season.
The 22-year old helped Barcelona to six trophies last season including the UEFA Champions League and edged past Ronaldo and teammate Xavi and Brazilian midfielder Kaka to take the award at a ceremony in Zurich.
Messi said: "I'm extremely happy. We've just ended a historic year, a perfect year in which we've won every competition we've played in. We just needed to take this last step and everything has worked out how we wanted. It's amazing."
Messi adds the award to the UEFA Club Footballer of the Year and the Ballon d’Or among many others he has snared in 2009.