SA minister quits over women's assault claims
The presidency said in a statement that head of state Jacob Zuma had "received and accepted" Manana's resignation.
"The President has thanked Mr Manana for his contribution to the work of government during his term of office," it added.
Manana was charged on 10 August and released on bail of R5,000 ($380, 320 euros).
A woman has accused him of kicking and punching her and her cousin at the exit of a nightclub in the early hours of 6 August.
Manana has not denied the allegations and has apologised, saying: "Regardless of the extreme provocation, I should have exercised restraint."
He is due to appear again in court on 13 September.
Violence against women is endemic in South Africa.
Every eight hours a woman dies after being attacked by a partner or relative, according to official statistics, and one woman in five will suffer at least one violent assault at some point in her life.
Source: AFP