The 35-year-old batsman will remain available for selection, but steps down shortly after Quinton de Kock took over as 50-over skipper for the recent England series.
De Kock has been named to lead South Africa against Australia, as the squad was announced on Monday with Kagiso Rabada included and no sign of AB de Villiers.
Pretoria-born Du Plessis had been the Proteas’ Test captain since de Villiers stood down in December 2016.
“The last season of my captaincy has been the most challenging to date as I had a lot of off-field issues that I devoted my energy towards,” du Plessis said in a statement.
“In a perfect world I would have loved to lead the team in the Tests for the rest of the season as well as the T20 World Cup, but sometimes the most important attribute of a leader is to be selfless.
It has been the greatest honour of my life to lead my country. Read my full statement here: https://t.co/QVRrvQGLmO pic.twitter.com/d5qH9pQJ9d
— Faf Du Plessis (@faf1307) February 17, 2020
“I am healthy, fit, energised and motivated and certainly see myself playing an important role in the squad for as long as I continue putting in winning performances for the team.
“(Captaincy) has been a rewarding, sometimes tough and other times a lonely road, but I would not replace the experience for anything, because it has made me the man that I am proud to be today.”
Du Plessis’ decision comes during a period of change in South African cricket with recent Test retirements of de Villiers, Dale Steyn, Morne Morkel, Vernon Philander and Hashim Amla.
South Africa plays Australia in three T20Is from Friday, followed by a three-match One Day International series from February 29 to March 7.
South Africa squad: Quinton de Kock (c), Temba Bavuma, Faf du Plessis, Rassie van der Dussen, David Miller, Pite van Biljon, Dwaine Pretorius, Andile Phehlukwayo, Jon-Jon Smuts, Kagiso Rabada, Tabraiz Shamsi, Lungi Ngidi, Bjorn Fortuin, Anrich Nortje, Dale Steyn, Heinrich Klaasen