Yoon’s attorneys argued at a preliminary hearing in February that his incarceration had been unfair, which the court accepted, leading to his discharge 52 times after his arrest.
After fighting with officers and prosecutors for weeks, he was the first South Korean president to be detained in a sun assault in January.
Yoon faces life in prison or even the death sentence if found guilty.
The 64-year-old previous head vacated the presidential residence on Friday and returned to his personal Seoul house, greeting supporters along the way.
He said in a statement,” I will now return to being an ordinary citizen of the Republic of Korea and I will look for a new path in the service of our country and our people.”
With Yoon’s resignation, South Korea will carry a snap election on June 3 to choose his son.
Han Duck-soo, the country’s speaking president, will serve as the nation’s interim leader until then.