The 25-year-old Argentina skipper was handed the prestigious FIFA prize in Zurich for a stunning 2012 in which he surpassed Gerd Muller's 40-year-old record with 91 goals in a calendar year over 69 matches.
Only France's Zinedine Zidane and Brazilian Ronaldo have had their hands on the trophy three times. It was also the sixth consecutive year that Messi had made the final three - voted by selected international journalists, football coaches and captains.
An emotional Messi, handed the trophy by Italian defender Fabio Cannavaro, said: "To tell you the truth this is really quite unbelievable. The fourth award that I have had is just too great for words.
"I would like to recognise my other colleagues from Barcelona; Andres it has been great to train and play alongside you. I would also like to recognise my friends in the Argentina team, everyone that has worked with me, coaches and staff and my family and friends. Also my wife and son.
"I'm more interested in team awards than I am about what I might win individually. There have been years where we won more titles that have been better."
The women's World Player of the Year award went to American Abby Wambach, beating off Brazilian Marta and international team-mate Alex Morgan.
Vicente del Bosque, who guided Spain to the 2012 European Championship two years after winning the World Cup, was voted men's coach of the year, while Pia Sundhage won the women's coach trophy after leading Wambach and the American team to gold at last summer's London Olympics.
But it was Messi, along with his stylish spotty jacket, who stole the show. His tricks dazzled the world's defences throughout last year as the football records tumbled.
In March he became the first player to score five goals in a Champions League match as Barcelona crushed Bayer Leverkusen 7-1.
The club's all-time scoring record was then broken with a hat-trick against Granada, and 14 goals in the 2011-12 Champions League broke the mark he had shared with former Manchester United striker Ruud Van Nistelrooy.
In May, Messi beat former Bayern Munich striker Mueller's record of 67 goals in a single European season, eventually finishing the campaign with 73.
Barca midfielder Cesc Fabregas wrote on Twitter: "Congratulations Leo, forth time as the best player of #ballondor, you deserve it. And also to @andresiniesta8, huge to be there."
Argentina team-mate Sergio Aguero tweeted: "Messi, Messi, Messi, Messi."
The FIFA Player of the Year award merged in 2010 with France Football's Golden Ball, given to the European player of the year.
The Golden Ball, or Ballon d'Or, was won three times by France's Michel Platini and Johan Cruyff and Marco van Basten of the Netherlands.
The 2012 FIFA-FIFPro world all-star team, voted by more than 50,000 players, included:
Goalkeeper: Iker Casillas (Real Madrid and Spain)
Defender: Daniel Alves (Barcelona and Brazil)
Defender: Sergio Ramos (Real Madrid and Spain)
Defender: Gerard Pique (Barcelona and Spain)
Defender: Marcelo (Real Madrid and Brazil)
Midfielder: Xabi Alonso (Real Madrid and Spain)
Midfielder: Andres Iniesta (Barcelona and Spain)
Midfielder: Xavi Hernandez (Barcelona and Spain)
Forward: Lionel Messi (Barcelona and Argentina)
Forward: Radamel Falcao (Atletico Madrid and Colombia)
Forward: Cristiano Ronaldo (Real Madrid and Portugal)