The 25-year-old Argentinian took the honour ahead of Barcelona team-mate Andres Iniesta and Real Madrid forward Cristiano Ronaldo.
Messi 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 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 all of my friends in the Argentinian national team, everyone that has worked with me, coaches and staff and my family and my friends. Also my wife and my son. Thank you."