The 91-year-old former president met with FIFA secretary general Jerome Valcke and chief local organizer Danny Jordaan, who brought the 18-carat, solid gold trophy to the Nelson Mandela Foundation buildings in Johannesburg. The meeting was held in private, with no journalists present.
Valcke said Mandela was one of the architects of the 2010 World Cup.
"For us there was no way that the trophy would arrive in the country and not be brought first to Mandela," Valcke said.
Jordaan said it was an "emotional and joyful moment" to bring the trophy back to Mandela, who is affectionately known as "Madiba" by South Africans, a traditional title adopted by members of his clan.
"It was so wonderful seeing Madiba in Zurich on the day South Africa won the right to host the 2010 FIFA World Cup, Jordaan said, "so happy with tears of joy rolling down his cheeks."
"So, it is quite an emotional and joyful moment to be back bringing the trophy to him, a symbol of world football with a global symbol of humanity."
FIFA and the Nelson Mandela Foundation did not release a statement from Mandela, but foundation chief executive Achmat Dangor said "We would like all South Africans and the world to see the trophy representing good."
Pictures of a smiling Mandela holding the World Cup in Switzerland in 2004 were beamed across the world and became the defining image of South Africa's successful bid.
Mandela announced later the same year that he was significantly cutting back on his public appearances and he is now rarely seen in public. It is still uncertain if South Africa's most famous citizen will appear at the World Cup's opening ceremony at the Soccer City stadium on June 11, although FIFA president Sepp Blatter has said he hopes Mandela will appear.
"We really hope that he will experience together with us the special moment celebrating South Africa's achievements in the stadium," Valcke said.
Mandela's schedule is not released in advance, and his staff have made no promises that he will attend World Cup events.
Rugby World Cup
Mandela has strong links to sport in South Africa after he appeared at the 1995 rugby World Cup final wearing the green and gold jersey of the Springboks, the country's national rugby team.
The jersey had previously been associated with the racist apartheid regime, and rugby was considered the sport of white South Africans before Mandela's act of reconciliation.
The Springboks went on to beat tournament favorite New Zealand in the final.
He also wore a South African football shirt when the country's national team won the 1996 African Cup of Nations in South Africa.
The World Cup trophy begins a countrywide tour of South Africa in Cape Town on Friday.