The court will now convey its decision to the detention center, which stated that it expects to release Yoon by the end of Friday.
On December 3, Yoon had unexpectedly declared martial law, accusing the opposition-controlled National Assembly of "paralyzing" his government.
The assembly rejected his martial law decree, forcing him to rescind it after six hours.
The country's highest court, the Constitutional Court, will now rule in the coming weeks on whether to uphold Yoon's impeachment or reinstate him.