The 54-year-old took charge after their triumph four years ago and is their first black coach.
However, he could not repeat their victory in New Zealand and they were beaten by the Wallabies this morning.
"There's a time to come and a time to go and I think the journey for me is over," he said.
"It was a brilliant journey, it's something you guys can not take away from me."
"To work with people like this, people that are passionate about their country, people who always put their bodies on the line and try to bring hope to poor people back home who will never have the privilege that most of you guys have."
Captain John Smit has announced his international retirement and is expected to join Aviva Premiership side Saracens.