Reuters reports young and old embraced as the funeral procession wound its way through the costal city's streets for hours, with some fans in tears and others cheering and drumming for a national hero who rose from barefoot poverty to become one of the greatest and best-known athletes in modern history.
"It's an irreparable loss for Brazil," said Brazil's newly sworn-in President Luiz Inacio Lula da Silva.
"Pele, in addition to being the best soccer player in the world, was a humble, simple man."
Pele died last week at the age of 82 after battling colon cancer for a year.
He was laid to rest at the city's Ecumenical Memorial Necropolis, a 14-storey vertical cemetery with views of the soccer field in Santos that made him a star.
Pele's funeral procession had left the city's Vila Belmiro stadium, home of Santos Football Club, on Tuesday morning.
Pele played from 1956 to 1974 for the team, scoring more than 1000 goals. During a 24-hour wake, fans queued for hours to pay their respects, even overnight.
One of Tuesday's most moving moments came when the firetruck bearing his coffin halted outside the home of Pele's 100-year-old mother. Crowds there applauded and chanted "Pele is our king," before holding a minute's silence.
Pele's sister Maria Lucia Nascimento, 78, watched in tears from a balcony and thanked the crowds in a brief TV interview.
Pele's son, Edson Cholbi Nascimento, addressed the crowd by the cemetery as fireworks greeted the arrival of the coffin and mourners sang the Santos anthem.
"I wanted on behalf of the whole family to thank you for all the love, the respect," he said. "It's an honour, it's a great pride. Once again thank you. Now he will rest."
The mausoleum where Pele now lies will be open to the public within seven days, the cemetery said.
On the streets of Santos, the city of 430,000 where Pele lived for most of his life, some struggled to come to terms with his loss.
"I'm still trying to get my head around this. No matter how much we prepare, we are never ready for the farewell," said Pele fan Marcelo Caverna.
"We are not just saying goodbye to our king, we are saying goodbye to a genius, a legend of the Brazilian people."
"You can see that the whole city has stopped. The whole world stopped," said mourner Ezequias Leonardo.
Fans of the late Brazilian football star Pele gather on the street as a firetruck transports Pele's coffin to the Santos' Memorial Cemetery in Santos, Sao Paulo state, Brazil on 3 January, 2023. Photo: AFP / Miguel Schincariol