Ordering Zuma to pay the costs of the latest court challenge, Judge President Mlambo said the South African leader's conduct was "clearly objectionable. and amounts to clear abuse of the judicial process".
The court found that Zuma must institute a commission of inquiry into state capture within 30 days, which would be headed by a judge appointed by Chief Justice Mogoeng Mogoeng, as per the "binding" remedial actions put forward by Madonsela.
"I think the important part of both of the judgments today (Wednesday), is that the courts have awarded the personal costs against the president", he said.
Naidoo said it was very important to note that the court ordered Zuma to personally pay the costs.
Upholding a recommendation by South Africa's corruption-fighting Public Protector, High Court Judge President Dunstan Mlambo said an application by Zuma challenging the inquiry was "ill-advised and reckless" and an abuse of the judicial process.
Zuma had tried to block the publication of the report arguing that he had not been granted enough opportunity to respond to the charges.
The report focused on allegations that Zuma's friends, the businessmen and brothers Ajay, Atul and Rajesh Gupta, had influenced the appointment of ministers.
The Guptas deny any wrongdoing.
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"There is the broader pattern of the president's conduct in litigation of defending what turns out, on the president's version, to have been the indefensible all along", said Judge President Dustan Mlambo.
Opposition leader Mmusi Maimane, who was at the court, welcomed the ruling.
On Friday, the same court ruled that Zuma's appointment of a state prosecutor was not valid and should be set aside immediately.
"The president shall take all steps, do all things and sign all documents which are necessary to give effect to the remedial action".
The commission is to complete its task and present its report within 180 days and Zuma is to submit a copy‚ with an indication of his intentions regarding the implementation‚ to Parliament, within 14 days of its release.
The ANC, he said, believes that Zuma will act in accordance with this judgment without delay in the interest of the country.
In her report titled State of Capture, former Public Protector Advocate Thuli Madonsela made several adverse findings against Zuma. Zuma is appealing that ruling.