The 25-year-old took the honour ahead of Barcelona team-mate Andres Iniesta and Real Madrid striker Cristiano Ronaldo.
The Argentina forward enjoyed a remarkable 2012 even by his own high standards, most notably surpassing Gerd Muller's 40-year-old record of 85 goals in a calendar year, finishing with an incredible 91.
Messi, wearing a polka-dotted dinner jacket and matching bow tie, 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."
Messi polled 41.60% of the votes, with former Manchester United ace Ronaldo taking 23.68% and Iniesta 10.91%.
Although he missed out on both the Primera Division and Champions League crowns, Messi racked up a host of personal achievements last year.
He scored an unprecedented 50 goals in a La Liga season, a record 14 goals in a Champions League season and became the first player to net five times in a Champions League match.
He also shattered the myth that he does not perform as well for Argentina as he does for his club by scoring 12 goals for his country in nine games.
Messi's fourth award took him past the three Fifa gongs won by former Brazil striker Ronaldo and ex-France midfielder Zinedine Zidane.