The iconic former Brazil international was presented with the trophy in Monday's ceremony in Zurich, having been ineligible to lift the prize during his playing career.
Pele struggled to hold back the tears after being awarded the first ever Fifa Ballon d'Or Prix d'Honneur.
The former Brazil international was ineligible to win the Ballon d'Or during his playing days as the original prize was reserved for European footballers, but Pele was acknowledged by the world governing body with the honorary award in the Ballon d'Or gala in Zurich on Monday.
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 teammates for his glittering playing career and admitted he was delighted to finally get his hands 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," he continued.
Pele was named FIFA Player of the Century in 2000 and part of the Fifa World Cup Dream Team two years later.
He later presented the 2013 Ballon d'Or trophy to Cristiano Ronaldo, who beat Lionel Messi and Franck Ribery to the prize.