Mkhwebane's spokesperson Cleopatra Mosana confirmed on Tuesday that Dlamini had resigned and cited personal reasons for his resignation.
"The Public Protector has accepted the resignation. His last day will be December 6," said Mosana.
Dlamini was appointed as the CEO at the office of the Public Protector in March, filling the vacancy left by Advocate Louisa Zondo, who resigned in November 2016. Zondo also resigned citing personal reasons.
Dlamini had joined the institution on a five-year fixed-term contract.
In a statement released when Dlamini was appointed, Mkhwebane said that Dlamini would bring a wealth of knowledge with him and that he would help "improve institutional performance, getting more out of little resources we have at our disposal".
The Public Protector said that Dlamini's career spanned nearly three decades in both the private and public sector, having held CEO positions at the Independent Communications Authority of South Africa and the National Gambling Board.
He also served as the deputy director-general responsible for corporate services and governance within the Department of Science and Technology, and was a special adviser to the minister of labour at the time.