Thousands of mourners crowded into a stadium in Soweto, near Johannesburg, where the campaigner was given a high-level send-off before her burial in Johannesburg.
Her casket was draped in the national flag, and South African President Cyril Ramaphosa delivered the eulogy.
The former wife of Nelson Mandela died earlier this month at the age of 81.
A controversial figure, Mrs Madikizela-Mandela was lauded for her role in the anti-apartheid struggle.
But she was later shunned by the political elite for endorsing punishment killings for government informers.
At the funeral, Mrs Madikizela-Mandela's daughter Zenani Mandela-Dlamini berated the "extreme cruelty" of those she said had led smear campaigns against her mother and isolated her - only to clear her name after her death.
"It is so disappointing to see how they withheld their words during my mother's lifetime, knowing very well what they would have meant to her. Only they know why they chose to share the truth with the world after she departed," Mrs Mandela-Dlamini said.
President Ramaphosa described Mrs Madikizela-Mandela as a symbol of resistance who laid bare the edifice of patriarchy. He apologised for only belatedly recognising her contribution.
"I'm sorry, Mama, that your organisation delayed in according you its honour, to this point in time and moment. As president, I will propose that we award you the highest order of our movement, you richly deserve to be awarded", Mr Ramaphosa said.
There were loud cheers when the radical Economic Freedom Fighters leader Julius Malema paid tribute to Mrs Madikizela-Mandela.
Mrs Madikizela-Mandela was a social worker when she met her future husband, then a prominent anti-apartheid campaigner, in the 1950s.
They were married for a total of 38 years but for almost three decades of that time, they were separated by Mr Mandela's long imprisonment. They had two daughters together.
After Mr Mandela was imprisoned by the apartheid regime, Mrs Madikizela-Mandela became an international symbol of resistance to apartheid.
She too was jailed for her role in opposing white minority rule.
To her supporters, she became known affectionately as "Mother of the Nation".
But Mrs Madikizela-Mandela also found herself mired in scandal for decades.
She was accused of conducting a virtual reign of terror in parts of Soweto by other members of the ANC in the late 1980s, and in 2003 she was convicted of fraud.
Orlando Stadium reverberated as thousands sang liberation songs, paying tribute to the freedom fighter known to many simply as Mama Winnie.
Supporters of various political parties who are often at odds with each put their differences aside to pay tribute to the anti-apartheid activist.
During the dark days of apartheid, Orlando Stadium in Soweto was always often associated with politicians delivering fiery speeches - and today was no different.
Winnie Madikizela Mandela's death managed to unite different political parties who are often at odds with each other.
Many agreed to put their differences aside to give her the send-off she deserved.
A reassessment of her contribution to South Africa's apartheid struggle has been playing out in local media.
While once she was shunned by South Africa's political elite, including her own party the ANC, in death she has been almost universally lauded.