Muzi Sikhakhane said Mr Zuma was subjected to "relentless cross-examination" and would "take no further part" in the proceedings.
The judge-led inquiry is investigating allegations that Mr Zuma oversaw a web of corruption during his term in office. He began testifying on Monday.
The 77-year-old was forced to resign as president in February 2018.
He was replaced by his then-deputy, Cyril Ramaphosa, who promised to tackle corruption in South Africa. Mr Ramaphosa described Mr Zuma's nine years in office as "wasted".
The lawyer, Mr Sikhakhane told the inquiry commission in Johannesburg: "Our client from the beginning... has been treated as someone who was accused."
He criticised the investigation, led by Judge Raymond Zondo, alleging that it was a "political process where the left hand doesn't know what the right hand is doing".
Who are the Guptas?
Mr Zuma had been due to give a final day of testimony on Friday but the inquiry has now been adjourned.
"I expected that he would cooperate," Judge Zondo said following Mr Zuma's withdrawal. "The first purpose was to give him an opportunity to tell his side of his story."
What is Mr Zuma accused of?
The allegations against Mr Zuma focus on his relationship with the controversial Gupta family, which has been accused of influencing cabinet appointments and winning lucrative state tenders through corruption.
He has also been accused of taking bribes from the logistics firm Bosasa, which is run by the Watson family. All the parties deny allegations of wrongdoing.
The scandal is widely referred to as "state capture" - shorthand for a form of corruption in which businesses and politicians commandeer state assets to advance their own interests.
On Monday, Mr Zuma gave a lengthy address in which he claimed the corruption allegations were a "conspiracy" aimed at removing him from the political scene.
"I have been vilified, alleged to be the king of corrupt people," he said.
He implied that the UK and US had been - and still were - part of an elaborate plot to discredit him, even as he tried to bring about political and economic change in South Africa.
Mr Zuma also said other foreign agents had tried to poison him, without naming them or offering any proof.
"I never did anything with them unlawfully," he said of the Gupta family. "They just remained friends, as they were friends to everybody else."
He also objected to allegations that he had allowed the state to be "captured" by the family. "Did I auction Table Mountain? Did I auction Johannesburg?" he asked.
On Tuesday, the former president said he had received death threats following his testimony.