Pele – who scored more than 1,000 goals in his career – died on December 29 at the age of 82 after a battle with cancer.
His body was placed in an open coffin in the middle of the Vila Belmiro Stadium in the Brazilian city on Monday.
Pele’s son Edinho helped carry his dad’s coffin onto the pitch at Santos, where the legendary striker played for 18 years.
Edinho was visibly emotional while Pele’s wife Marcia Aoki was comforted by Lula and Fifa president Gianni Infantino also paid his respects.
Some 230,000 mourners including the new Brazil president Luiz Inácio Lula da Silva l filed past after forming a 2km queue.
Many camped outside to ensure they could pay their respects to their hero.
And after 24 hours, mass was held at the stadium before the coffin was draped in a Brazil flag guarded by army soldiers this morning for the procession through the city.
Pele’s coffin was carried through the streets and passed in front of the home of his 100-year-old mother, Celeste.
It was taken into the cemetery as bands played the Santos team’s official song, and a Catholic hymn.
Before the black casket arrived, attendees sang samba songs that Pele had liked.
The burial took place at the Memorial Necropole Ecumenica and only his family attended.
Pele reportedly chose a burial site on the ninth floor of the cemetery will allow him to “watch over” the Santos stadium.
His final resting place is in a unique “vertical cemetery” in a 14-floor building that includes 14,000 vaults, a waterfall and a car museum.
It includes crypts, rooms to hold services, a crematorium, and a mausoleum “for families who want to preserve their legacy in a more personal and private way”.
It even contains a tropical garden that includes a small rooftop cafe and a waterfall also.
Pele burst onto the global stage in 1958 and helped Brazil win back-to-back World Cups four years later.
His success in 1970 ensured he became and remains the only person to win three World Cup tournaments as a player.
At club level, Pele enjoyed 18 sensational years with Santos, the team he made his debut for aged 15.
Overall, he scored a staggering 1,279 goals in 1,363 games, including friendlies, which is recognised as a Guinness World Record.
He also managed a remarkable 77 goals in 92 games for the national team – a record equalled by Neymar at the recent World Cup.