The North Gauteng High Court ordered Zuma to personally pay the costs of the review of former public protector Thuli Madonsela's recommendations on alleged state capture.
Zuma said on Tuesday night that Chief Justice Mogoeng Mogoeng had selected Deputy Chief Justice Raymond Zondo to head the commission of inquiry.
Soon after the ruling, Zuma applied to appeal the ruling, saying the decision to call for a commission of inquiry into state capture was based on "untested suspicions" and "prima facie evidence".
Madonsela said she had clarity on what the terms of reference should be: what she investigated. "There is no room to expand the commission to include what was never investigated", she said.
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The report called for a full-scale commission of inquiry with wide reaching powers.
"By making more resources available‚ it is my honest hope that the commission‚ will be able to reach many of those areas of concern that may not have been reached by the Public Protector's investigation‚ but form part of what she might have investigated‚ had she had sufficient resources to do so".
In a statement from the South African Presidency, it said that Ramaphosa, who led the SA delegation in 2017, will again this year lead a team comprising government ministers and business leaders, with Minister of Finance Malusi Gigaba being the lead minister and co-ordinator.
"There should be no area of corruption and culprit that should be spared the extent of this commission of inquiry", he continued, before adding that he expects everyone to cooperate with the inquiry".
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"There is nothing under the sun stopping president Zuma or any president from initiating twenty judicial inquiries into state capture by white monopoly capital".
UDM leader Bantu Holomisa on Wednesday wrote to Zondo. Zuma wanted Madonsela's remedial action set aside.
"It is the work of the former Public Protector, her findings and remedial actions which saw the UDM and other parties in and out of court to force the matter to fruition; we have at last reached that point, where the truth will be revealed", wrote Holomisa.
"Such broad terms would have the potential to bog down the inquiry, rendering it ineffective, but whether Zuma will emerge from this week's ANC conference in East London with enough power to influence the terms of reference will be instructive", she said.
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"But this one is specifically about the Gupta family, the president and his son", said Madonsela.