The board of Cricket South Africa (CSA) suspended chief executive Gerald Majola on Saturday, pending an independent disciplinary inquiry.
The board also agreed to follow the recommendations of the Nicholson Inquiry into a bonus scandal that has engulfed the administration of the game in the republic.
The Nicholson Inquiry, appointed by sports minister Fikile Mbalula, found earlier this month that Majola had "surreptitiously" received 1.8 million rand ($237,000) in unauthorised bonuses from the Indian Premier League, as well as irregular travel expenses, in contravention of the Companies Act.
Majola had initially been cleared of any serious wrongdoing by a CSA inquiry headed by acting president AK Khan, who has since resigned.
"The board of directors of CSA considered the recommendations of the Nicholson Committee of Inquiry and, after lengthy deliberations, have resolved to rescind all the findings of the Khan commission and to suspend Majola with immediate effect pending a disciplinary inquiry," board member Oupa Nkagisang told a news conference on Saturday.
The CSA board elected a new acting president to replace Khan in experienced administrator and transformation committee chairman Willie Basson. Jacques Faul of the North-West province was appointed acting CEO.
Judge Chris Nicholson said on March 9 that Majola should face an independent disciplinary inquiry as well as possible criminal charges.
Former International Cricket Council (ICC) president Ray Mali, who chaired Saturday's CSA meeting, said outside experts would handle Majola's disciplinary process.
"We will have to get eminent people, reputable people, so that there are no comebacks. The board will meet on March 30 to decide who will head the disciplinary inquiry, but it has to be an independent person," Mali said.
Mali added that the board had considered dissolving itself.
"The entire issue of dissolving the board did come up, but that can only be decided by the affiliates and provinces," he said. ($1 = 7.5948 South African rand)