Messi beat Real Madrid and Portugal"s Cristiano Ronaldo and Barcelona teammate Xavi to the award which is voted on by a panel of journalists from across the world.
The 22-year old bettered his second-place finish last year and his third-place in 2007.
"Honestly, I knew that I was among the favourites because Barcelona had a fruitful year in 2009," Messi was quoted as saying by the magazine.
"But I didn't expect to win with such a margin. The Golden Ball is very important to me. All the players who won it were great players, and some great players never won it," he added.