The former Brazil international's 21-year career pre-dated the advent of the Ballon d'Or, and Pele was acknowledged by the world governing body with the honorary award.
Pele scored 1,281 goals in his career, and is the only man to lift three World Cups titles, having triumphed in 1958, 1962 and 1970.
Speaking at the awards ceremony in Zurich, the 73-year-old thanked his team-mates and admitted he was delighted to finally get his hand on the trophy.
"I promised to my family that I would not cry but I am emotional," he said. "First of all I have to thank God for giving me the health to play so many years.
"Of course I did not play alone. When we talk about my friends people remember the players but we don't have to forget the guy who cleaned the shoes, the masseur - I had a lot of good people on my side. I have to share with them all this trophy.
"I got so many trophies and prizes but I was jealous because all of those guys who got the Ballon d'Or, which I couldn't get because I didn't play in Europe. Now I thank God that I can complete my trophies at home."
Pele was named FIFA Player of the Century in 2000, and part of the FIFA World Cup Dream Team two years later.
