Particularly the argument by the President, as quoted in the "State of Capture" report, that he could not be a jury and a judge in his own case, referring to why he could not initiate an investigation into allegations implicating him, is central to the logic, now accepted by the court, of the remedial action that while he should appoint a judge to head the commission he should not be the one to select the judge.
The report by then graft ombudsman Thuli Madonsela released in November a year ago ordered a judicial inquiry into allegations that the Guptas may have influenced the appointment of cabinet members in Zuma's administration and received special treatment for a coal business linked to the family and Duduzane Zuma, the president's son.
Pretoria's High Court ordered Mr Zuma to set up a judicial inquiry, calling him "seriously reckless" for challenging recommendations by a watchdog in a case against him.
On the president's contention that there was a typing error, Mlambo suggested that President Zuma's subsequent statements nullified that claim.
The court ordered that once the inquiry is set up, it should complete its task and present its report to Zuma within 180 days.
The ruling African National Congress will choose its new leader, to replace embattled Jacob Zuma over the weekend.
"This is unprecedented but it also reflects the extent to which the courts might have taken a dim view of the president's abuse of legal process", Phephelaphi Dube, director of the Centre for Constitutional Rights, said by phone.
Zuma had tried to block the publication of the report arguing that he had not been granted enough opportunity to respond to the charges.
He said he believed it was "hopeless" for Zuma to consider appealing the judgments.
He has also faced allegations that his close links to the family have been used to influence the appointment of key ministers.
Mlambo said a judicial commission was best suited to investigate the allegations against Zuma. Both Zuma and the Guptas have denied the accusations.
The report's author, Thuli Madonsela, told Reuters after the verdict: "An allegation that the state has been captured in the interests of the president and his friends is an allegation that needs to be investigated immediately".
The ruling dealt a heavy blow to Zuma who has been seeking an order by the North Gauteng High Court to have Madonsela's remedial actions, contained in her State of Capture Report, reviewed and set aside.