Pele never won the Ballon d'Or, which began in 1956 as he never played in Europe.
FIFA inaugurated their own world footballer of the year award in 1991 but Pele had long since retired. The FIFA and Ballon d'Or awards were merged in 2010.
"I promised to my family that I would not cry but I am emotional," Pele said as he collected his award.
"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."
France Football magazine, which founded the Ballon d'Or said: "For regulation reasons the king is not on the list of Ballon d'Or winners, an anomaly that was corrected in 2013."
Pele is believed to have scored 1281 goals in 1363 games in his career. He is the only player to have won three World Cups and he scored 77 goals for Brazil in 92 appearances.