Aged just 25, Messi has now been voted the world's best player for an unprecedented fourth straight year as the outstanding talent of his generation.
Messi beat his great rival Cristiano Ronaldo of Spanish champion Real Madrid and Barcelona teammate Andres Iniesta, who starred as Spain won the 2012 European Championship.
"To tell the truth, this is really unbelievable to get the fourth award. I am so nervous," a typically low-key Messi said, in Spanish, though he wore a black tuxedo jacket with a white-spotted pattern in an unexpectedly flamboyant touch.
Messi's fourth award lifted him above three-time FIFA winners Zinedine Zidane of France and Brazil's Ronaldo. The old Ballon d'Or trophy for players in Europe was won three times by France great Michel Platini, and Netherlands forwards Johan Cruyff and Marco van Basten.
Messi received 41.60 per cent of the points in votes cast by national team coaches and captains plus invited journalists, who gave their top-three lists from an original slate of 23 players.
Ronaldo got 23.68 per cent and Iniesta 10.91 per cent. Ronaldo scored the highest proportion of his points from media, while Messi scored best with coaches.
"Whether I win or not it doesn't matter, it's a privilege to be here," Ronaldo, the 2008 winner, said earlier when sharing a news conference platform with Messi. The two national team captains downplayed down their rivalry, though neither chose to vote for the other.
Messi led a dominating night for Spanish teams and the United States women's Olympic champions at FIFA's annual celebration of world football.
Vicente del Bosque won the coaching award for guiding Spain to its third straight major tournament victory at Euro 2012.
Abby Wambach, who scored five goals at the London Games, was named the best women's player. Teammate Alex Morgan was also nominated to become the first American winner since Mia Hamm got the 2002 award. Canada's Christine Sinclair finished fifth after her breakout season that saw her score a Canadian-record 23 goals, including six at the London Olympics
Pia Sundhage, who also led the U.S. team to gold at the 2008 Beijing Olympics, won the coaching award for women's football — then sang from the stage in her acceptance speech.
Canada's coach John Herdman was sixth in voting for top women's coach.
Barcelona players have now won 10 times in the 22 years that FIFA has awarded a world's-best prize. In 2010, the FIFA world player honour merged with the Ballon d'Or prize awarded to Europe-based players since 1956 by 'France Football' magazine.
Messi's goal-scoring record shone in a relatively disappointing year by the high standards of the Catalan club which won just one trophy, the Spanish Cup, in 2012.
Madrid, sparked by Ronaldo's 46 league goals, took back the La Liga title and Barcelona went down to a shock defeat in the Champions League semifinals to eventual winner Chelsea.
Still, Messi defied critics who believe his standards drop for Argentina by scoring 12 goals for the national team in 2012, including five at a goal-a-game rate in 2014 World Cup qualifiers to ensure it leads the South American qualifying group.
Messi's goals also helped give Barcelona, under new coach Tito Vilanova, a runaway lead in the Spanish league this season thanks to a record start of 17 wins and one draw.
Wambach's goals at the Olympics earned her the FIFA prize at the age of 32. She placed third last year.
"Thank you for challenging me every day, Alex especially," Wambach said to her rivals on the three-player shortlist, Morgan and five time winner Marta of Brazil.
Wambach got 20.67 per cent of the voting points on a 10-player original slate. Marta scored 13.50 per cent and Morgan tallied 10.87 per cent.
The U.S. players had been serenaded from the stage by Sundhage, who sang a verse of the Bob Dylan song 'If Not For You' on receiving the coaching award. Sundhage beat two male candidates: Norio Sasaki of Olympic silver medallist Japan, and Bruno Bini of France.
Sundhage returned to Sweden to coach her home national team after the Olympics, and added more sparkle to the FIFA event by wearing a black and glittery 'Sweden 2013' T-shirt to advertise its hosting of the next women's European Championship.
Del Bosque was a more serious, but equally respected, winner of the men's coaching award. Madrid coach Jose Mourinho, who did not attend, was second and former Barcelona coach Pep Guardiola was third.
The Puskas Award for the best goal in 2012 was won by Miroslav Stoch of Fenerbahce. The Slovakia forward scored with a long-distance volley after a corner in a Turkish league game against Genclerbirligi in March.
Brazil star Neymar was beaten in the fans' online vote as he sought to win for a second time. He placed 13th in Ballon d'Or polling.
All three Ballon d'Or nominees featured in a World XI lineup chosen by the FIFPro group of players' unions comprising 50,000 members worldwide.
They selected a team composed entirely of players from Spanish clubs, with nine repeating their selection from one year ago.
Madrid captain Iker Casillas was selected as goalkeeper. In defence, Barcelona's Dani Alves and Gerard Pique lined up alongside Madrid's Sergio Ramos and Marcelo.
Iniesta was named in midfield with Barcelona teammate Xavi Hernandez and Madrid's Xabi Alonso. Messi led the attack with Ronaldo and Radamel Falcao of Atletico Madrid. Marcelo and Falcao replaced Manchester United pair Nemanja Vidic and Wayne Rooney from the 2011 team.
Sepp Blatter made the FIFA presidential award to Franz Beckenbauer, who captained and coached West Germany to World Cup victories, and then led the local organizing committee of the 2006 World Cup in Germany. Uzbekistan won the fair play award for its teams' good disciplinary record.