Earlier this week Zuma accused a close comrade in the liberation struggle, Ngoako Ramatlhodi, of being a spy for the apartheid government and foreign intelligence services. He said the ANC had been infiltrated by other spies.
Zuma will now be allowed to submit written statements to the inquiry on incidents where other witnesses have implicated him in wrongdoing, as opposed to being questioned by a legal team in public.
Zuma will return to give evidence in public at a later stage, but it is not yet clear when.
Zuma’s lawyer, Muzi Sikhakhane, told commission chair judge Raymond Zondo that Zuma had been subject to a "relentless cross-examination".
"This animal called corruption is amorphous, we don’t know who is actually corrupt,” Sikhakhane added.
Zuma threatened on Friday to pull out of the inquiry but withdrew that threat when his demand for a more lenient form of questioning was granted.
Analysts say that if the inquiry fails to link Zuma to serious wrongdoing, it could dent President Cyril Ramaphosa’s credibility.
Ramaphosa suffered his own setback on Friday when public protector Busisiwe Mkhwebane said he had "deliberately misled" parliament about a donation he received for his 2017 election campaign for the ANC leadership.