Revd Canon Mpho Tutu-Van Firth said she was forced to leave her role in the Anglican Church because it does not recognise same sex marriages.
Clergy are forbidden from entering a gay marriage and she would have likely been stripped of her licence to practice had she not stood down herself.
It was a "dignified" exit from the Church, she said.
"Because the South African Anglican Church does not recognise our marriage, I can no longer exercise my priestly ministry in South Africa.
"The bishop of the diocese was instructed to revoke my licence. I decided that I would give it to him rather than have him take it."
Gay marriage has been legal in South Africa since 2006 but the Anglican Church in the country says marriage can only be between one man and one woman.
Tutu married Marceline Tutu-Van Furth earlier this year and the couple are currently on honeymoon.
Archbishop Desmond Tutu, 84, attended the wedding.
