Judge Mabel Jansen has written to President Jacob Zuma and to Justice Minister Michael Masutha informing them of her resignation with immediate effect.
Jansen, on special leave since May last year, made a string of Facebook comments, in which she said 99% of the criminal cases she heard were "of black fathers/uncles/brothers raping children as young as five years old".
Masutha said yesterday he had acknowledged the letter and thanked her for her service.
Jansen was on special leave following comments she made that resulted in a complaint to the Judicial Service Commission, which was processing the complaint.
Masutha said her resignation would remove a need for a protracted disciplinary process.
Jansen said: "Want to read my files: rape, rape, rape, rape, rape, rape of minors by black family members. It is never-ending."
In private direct messages Jansen said in black culture "a woman is there to pleasure" men, that women tell their children it is their father's birthright to be the first and that gang rapes of babies, mothers and daughters were a "pleasurable pastime".
Masutha said the escalating rate of racial incidents in the country had required the government to take steps, including the Hate Crimes and Hate Speech Bill.
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