"Maligning the public protector besmirches not only the ruling party, but the entire country. We are proud that South Africa has an Office of the Public Protector," the Nobel Peace Prize winner and his daughter said in a joint statement.
"The contempt being shown to the public protector by the ruling party underlines the slippery moral slope South Africa has descended since the days of hope and promise under President Nelson Mandela."
Madonsela and the African National Congress have been locked in a war of words following the leaking of a letter she had written to President Jacob Zuma over his response to her report on the upgrades to his Nkandla home.
In her letter she reportedly cautioned him that he was second-guessing her recommendations that he repay part of the money spent on features unrelated to security, such as a swimming pool, cattle kraal, amphitheatre, and visitors' centre.
In his reply to Madonsela's report on Nkandla, Zuma indicated that Police Minister Nathi Nhleko should determine if he should repay any of the money.
The Tutus said the creation of a public protector in the new South Africa reflected the country's evolutionary progress as a nation.
South Africa now had a public protector whose job it was to investigate any conduct in state affairs or the public administration where impropriety or prejudice was suspected or alleged.
"Accountability is not just a word. It is a foundation stone for good leadership, responsibility, trust, justice and respect," they said.
When Mandela was called to appear before the Pretoria High Court to defend a decision to investigate alleged graft and racism in South African rugby, many people thought he would fend off the summons on technical grounds.
"But he chose to appear in court to demonstrate his accountability to the rule of law and administration of justice.
"If the ruling party has issues with the process the public protector has followed in respect of the investigation into the hideous public spending on improvements to President Zuma's accommodation in Nkandla, or with the findings, its obligation is to approach the courts for a remedy," they said.
The pair applauded Madonsela's courage and called her a woman of integrity who served her country without fear or favour.
"We, humbly, suggest that all South Africans take pride in a job well done, and let Thuli Madonsela get on with her work."