Messi became the sixth Barcelona player to take the award and the first since Brazilian Ronaldinho in 2005. He beat last year's winner Cristiano Ronaldo into second place while Barcelona midfielder Xavi Hernandez finished third in the poll results released by France Football.
Hailed by Argentina great Diego Maradona as his successor, Messi won an unprecedented treble in Spain last season with Barcelona as the Catalan side swept the Champions League, the Spanish title and the Copa del Rey.
Messi, who tallied 473 of a possible 480 points, largely dominated the voting and won with a record-margin of 240 points. Real Madrid winger Ronaldo had 233 and Xavi had 170.
"Honestly, I knew that I was among the favorites 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."
The 22-year-old Messi, the first Argentine to win the prestigious trophy, was the top scorer in last year's Champions League with nine goals, including his superb header in the 2-0 victory over Manchester United in the final.
Barcelona had three players in the Top 5 with Andres Iniesta taking fourth ahead of former Barca player Samuel Eto'o.
In an outstanding season, Messi netted 38 goals in 51 games in all competitions, often leaving defenders in his wake with a combination of speed, exceptional dribbling abilities and his effective left-footed strike.
Messi, who leads Argentina to next year's World Cup in South Africa, recently signed a new contract with Barcelona through 2016 and has a buyout clause of 250 million euros ($368 million) included.
Messi had a good start to this season - already scoring nine goals - and put on a great display to help his club defeat archrival Real Madrid 1-0 last Sunday.
"It won't be easy to confirm after a year like the one we just went through," Messi said. "I hope the next one will reach the same standards. But to win the Golden Ball two years in a row is not an easy thing."
After starting club football in 1995 at Argentina's Newell's Old Boys, Messi, who suffered from a growth hormone deficiency when he was a child, joined Barcelona's Under-14 team in 2000 after the Spanish club offered to pay for his treatment.
The diminutive forward - 1.69 meters and 67 kilograms (5-feet-7; 148 pounds) - was part of the Argentina team at the World Cup 2006 before claiming the Olympic gold in Beijing in 2008.
France Football's award was decided by an annual poll of football journalists from a shortlist of 30 players.
The 24-year-old Ronaldo won the Premier League title with Manchester United in 2009 before signing with Real Madrid for 93 million euros.
Named best player at the 2008 European championship, where Spain won its first major title in 44 years, midfielder Xavi was also a key element in Barcelona's treble in 2009, playing 35 Spanish league games and 14 of the 15 European matches of his club.
