The 24-year-old Argentinean beat team-mate Xavi and Real Madrid's Cristiano Ronaldo to the title of the world's best player.
Messi, man of the match in the Champions League final in 2011, also won the La Liga, Spanish Supercopa, UEFA Super Cup and Club World Cup last year.
Messi's Barcelona team-mate Xavi paid tribute to the young Argentinean, predicting a bright future for him and proclaiming that Messi will be named amongst the greats in football.
He said: "He's still young, only 24, and I think he's going to break all the records that exist in this sport.
"He's going to be one of the best footballers in the history of the sport."
Manchester United's Wayne Rooney and Nemanja Vidic were both included in the world XI dominated by Spain-based players.
The FIFPro World XI was: Iker Casillas (Real Madrid), Dani Alves (Barcelona), Gerard Pique (Barcelona), Sergio Ramos (Real Madrid), Nemanja Vidic (Man Utd), Andres Iniesta (Barcelona), Xabi Alonso (Real Madrid), Xavi (Barcelona), Lionel Messi (Barcelona), Cristiano Ronaldo (Real Madrid), Wayne Rooney (Man Utd).
Rooney said at the gala: "It was a great year and the highlight was winning the Premier League for the 19th time, which was a great moment for the club."
Barcelona's Pep Guardiola was named coach of the year; Japan's women's World Cup-winning captain Homare Sawa the women's player; Japan's (male) manager Norio Sasaki coach of the year for women's football; the Japanese FA were awarded the FIFA fair play award; Brazilian 19-year-old sensation Neymar won the FIFA Puskas award for the best goal of 2011.
Lionel Messi factfile:
1987: June 24 - Born in Rosario, Santa Fe, Argentina.
1995: Joins Newell's Old Boys.
1998: Diagnosed with a growth hormone deficiency at age of 11.
2000: Moves to Barcelona, aged 13.
2003: November 16 - Makes first-team debut in friendly at Porto at the age of 16.
2004: October 16 - Appears in first official Barca match, aged 17, in 1-0 derby win at Espanyol.
2005: May 1 - Becomes youngest player to score for Barcelona by netting against Albacete.
June - Helps Argentina to World Youth Championship triumph in Holland. Messi is competition's top scorer and is named player of the tournament.
August 17 - Makes full Argentina debut as second-half substitute in Hungary, only to be shown a red card within two minutes.
September - Granted EU passport by Spanish government.
2006: May - Helps Barca retain Primera Division title and win Champions League, although he misses out on Champions League final win over Arsenal in Paris due to injury.
June 16 - Becomes youngest player to represent Argentina at a World Cup with substitute appearance against Serbia & Montenegro. Also nets final goal in 6-0 win to become fifth youngest goalscorer in World Cup history.
2007: July - Named Young Player of the Tournament after helping Argentina to Copa America final, where they lose to Brazil.
December 2 - Finishes third behind Kaka and Cristiano Ronaldo in Ballon d'Or voting.
December 13 - Again misses out to Kaka, this time finishing second to the Brazilian in FIFA World Player of the Year poll.
2008: July 3 - Included in Argentina squad for Olympic Games in Beijing, prompting protracted dispute between the Argentinian federation and Barcelona, who want the player available for Champions League qualifiers.
August 7 - Barca announce they will allow Messi to remain with Argentina squad for the duration of the Olympics.
August 23 - Helps Argentina to gold with a 1-0 victory over Nigeria in the final in Beijing's Bird's Nest stadium.
December 2 - Finishes second behind Cristiano Ronaldo in Ballon d'Or voting.
2009: May 27 - Scores second goal as Barcelona beat Manchester United 2-0 to win Champions League final in Rome. Also helps Barca win the Primera Division and Copa del Rey titles in an unprecedented treble.
October 14: Helps Argentina reach the World Cup finals with 1-0 win in Uruguay.
December 1: Wins Ballon d'Or.
2010: April 6 - Scores four as Barcelona knock Arsenal out of the Champions League.
May - Equals Ronaldo's club record of 34 goals in a league season as Barca win the Primera Division title again.
June - Plays every game as Argentina reach quarter-finals of the World Cup before being knocked out by Germany.
November 20 - His second hat-trick of the season in Barca's 8-0 win over Almeria takes him to 100 goals in La Liga.
2011: January 10 - Wins FIFA Ballon d'Or.
May: Ends campaign having helped Barca to Champions League and Primera Division glory. Finishes the season with 50 goals in league, Copa del Rey and Champions League action.
August - Named Argentina captain by new coach Alejandro Sabella.
December - Part of the Barcelona squad which wins the Club World Cup in Japan.
2012: January 9 - Retains FIFA Ballon d'Or prize.