Two of its partners, Sipho Malaba and Dumi Tshuma, had resigned, KPMG announced on Friday afternoon.
Between them, the two had been at KPMG for more than a quarter of a century.
KPMG said disciplinary cases against both had included "failure by the partners to comply with the firm’s policies and procedures regarding the disclosure of relevant financial interests" related to VBS Mutual Bank.
Since VBS was placed into curatorship and its books effectively opened it has emerged that some R900 million of its supposed deposits could not be traced.
There have also been allegations that insiders benefitted, and that some were extended loans despite conflicts of interest.
There has been no evidence that such benefits or loans flowed to the bank's auditors, either KPMG or (since dismissed) internal auditors PwC.
But there has been extensive evidence that the VBS books – signed off by its auditors – were in a terrible state.
In mid 2017, legal papers filed by the Reserve Bank show, VBS had a shortfall of R250 million. It turned out that VBS had accidentally paid that money out "due to internal control failures in a branch".
There had "inept risk management functions and practices" the Reserve Bank said.
And sometimes VBS had managed hundreds of millions of rands using consumer-grade desktop software.
Before it was placed in curatorship, regulators pointed out the VBS relied on one specific area of its business to drive profits: its fuel-guarantee and contract-finance business.
Once the books were opened to its new curator, the details of how those business lines were managed came to light.
"Excel spreadsheets are used to manage the contract finance and fuel guarantee books of the bank," the Reserve Bank told the high court in a filing. "In addition to these being susceptible to manipulation, it is highly unusual for a bank to manage these contracts by means of an Excel spreadsheet."