Messi, the talented Barcelona forward, sent last year's winner Cristiano Ronaldo into second place, making him the sixth Barcelona player to take the award but the first for four years - since Brazilian playmaker Ronaldinho.
Messi became the first Ballon D'Or winner from Argentina, eclipsing Ronaldo by a record 240-point margin. The award's 96 jurors gave Messi 473 points out of a possible 480, a near unanimous verdict, the magazine said on its website.
Messi told France Football: "There's lots of emotion - the Ballon d'Or is very important for me. I know I appeared among the favourites because Barcelona had a profitable year.
"For me it's a big honour to win - but also to become the first Argentinian in history to receive the trophy. I dedicate it to my family, they were always present when I needed them and sometimes felt even stronger emotions than me.''
Messi recently signed a two-year contract extension with the European champions until 2016 - an improved deal which includes a buy-out clause worth 250million euros (£228million).
The 22-year-old Argentinian won an unprecedented treble last season as Messi's Catalan side won the Champions League, the Spanish title and the Copa del Rey. Messi was the top scorer in last year's Champions League with nine goals, including a header in the 2-0 final defeat of Manchester United in Rome.
Messi also hit 23 goals in the league and six in the King's Cup. As the leading light in the world's best team this year, it had been widely expected Messi would snare the Ballon d'Or in the lead up to Tuesday's announcement.
Ronaldo (233 votes) was the only non-Barcelona player in the top four, with Xavi (170) and Andres Iniesta (149) next in the list. Former Barca striker Samuel Eto'o - now with Inter Milan, was fifth on 75, 17 votes clear of Real's former AC Milan playmaker Kaka.
Barcelona's Zlatan Ibrahimovic, who moved in the opposite direction to Eto'o, polled 50 - before a quintet of English-based players. Manchester United and England striker Wayne Rooney and Chelsea forward Didier Drogba were eighth and ninth, with Liverpool midfielder Steven Gerrard completing the top 10.
Liverpool striker Fernando Torres was 11th, Arsenal midfielder Cesc Fabregas 12th, with Manchester United winger Ryan Giggs - who netted his 100th Premier League goal at Portsmouth on Saturday, finishing 14th.
Barcelona's Thierry Henry, heavily criticised for his handball in France's World Cup play-off win over Republic, completed the top 15. Manchester United defender Nemanja Vidic shared 16th place with eight points alongside Sevilla striker Luis Fabiano and Real Madrid goalkeeper Iker Casillas.
Atletico Madrid's Diego Forlan polled seven and Bordeaux striker Yoann Gourcuff six, while Arsenal midfielder Andrei Arshavin and Chelsea counterpart Frank Lampard shared 21st with five alongside Inter keeper Julio Cesar.
Inter Milan's Maicon (four), Juventus' Diego (three), Valencia's David Villa and Chelsea defender John Terry (two), and Bayern Munich's Franck Ribery and Barcelona's Yaya Toure (one) completed the star-studded list.