Yun plunged the country into political chaos with his December 3 proposal to suspend civilian rule, which lasted just six hours before lawmakers defied the armed forces in parliament and rejected it.
He was removed from office soon after, and earlier this month became the first sitting South Korean head of state to be arrested.
This followed a week-long detention at his residence, where his elite bodyguards resisted attempts to detain him.
Prosecutors said they "today indicted Yoon Suk Yol for detention on charges of being the leader of an insurgency."
He has been held at the Seoul Detention Center since his arrest, and the formal detention charge means he will now be held behind bars until his trial, which is due to take place within six months.
The indictment was widely expected after the court twice rejected prosecutors' requests to extend his detention order while the investigation was ongoing.
"After a thorough review of the evidence obtained during the investigation, prosecutors concluded that it was appropriate to charge the defendant," they said.
The need to keep Yun behind bars was justified by the "continuing risk of destruction of evidence," prosecutors said.
The specific charge - of leading an uprising - is not covered by presidential immunity, they added. | BGNES
