Suspended City of Cape Town transport director Melissa Whitehead resigned on Wednesday afternoon.
Whitehead’s resignation comes after she was found guilty in a disciplinary hearing.
The city said Whitehead had also faced a second, unrelated, disciplinary hearing which related to a tender for electric buses.
She was suspended earlier this year after facing allegations of improper conduct, after an investigation report from legal firm Bowman Gilfillan.
The report found suspected acts of corruption which related to her allegedly improperly appointing UK consultants to set up the transport authority, and her alleged connections to the consultants before they were awarded the contract.
It was previously reported that she was paid almost R5m while sitting at home for the past 19 months.
The Sunday Times reported that the city council wanted some of the money back and had instructed officials to reclaim more than R400,000 from Whitehead and a former council lawyer, and to launch two new disciplinary procedures against her for alleged misconduct.