"Minister of Police, Mr Fikile Mbalula has taken a decision to withdraw the appeal lodged at the Supreme Court of Appeal, on the case brought by Helen Suzman Foundation and Freedom Under Law NPC," the department of police said in a statement.
Last month the High Court in Pretoria reviewed and set aside Ntlemeza's appointment as the head of the Hawks.
Ntlemeza was appointed permanently to the position by former Police Minister Nathi Nhleko in September 2015, despite Judge Elias Matojane's ruling that Ntlemeza "lacks integrity and honour".
The Freedom Under Law and Helen Suzman Foundation brought arguments before the court saying Ntlemeza was not fit and proper to hold office – the court agreed with them.
The court ruled that Ntlemeza lacks the requisite honesty, integrity and conscientiousness to occupy any public office, and declared his appointment invalid and unlawful.
The then police minister appealed the ruling.
However, on Wednesday when the matter was to be heard in court, Mbalula who has recently taken over the portfolio decided to withdraw the appeal.
"The minister of police, will on Thursday the 13th April 2017 meet with the top management of the Directorate for Priority Crime Investigation (Hawks) and inform them of his decision," the police department said.
Mbalula has already informed Ntlemeza of this decision and asked for his observance.
The general who is now expected to leave office was not immediately available for comment.