The decision by the Seoul Central District Court came a day after Yoon's legal representatives filed a petition seeking a review of the legality of Yoon's detention, Yonhap news agency reported.
The previous day, investigators detained Yoon for questioning over his December 3 martial law declaration after he ignored three summonses to appear for questioning in the investigation.
Thursday's court decision rejected claims from Yoon's side that the detention warrant against him, issued by the Seoul Western District Court, was invalid.
Yoon had repeatedly argued that the case should have been handled by the Seoul Central District Court instead, as his lawyers claimed prosecutors would eventually bring the case there.
The court also rejected claims from Yoon's side that the Corruption Investigation Office for High-ranking Officials (CIO) lacks jurisdiction over insurrection, recognising the office's authority to investigate such cases.
The court also rejected arguments that police personnel engaged in illegal activities in the detention process and that the martial law declaration, involving only a small number of unarmed personnel entering the National Assembly, did not constitute a breach of the constitutional order.
While the court review was in progress, Yoon's 48-hour detention period had been put on hold since about 2 p.m. when investigators submitted documents, including evidence, to the court. The detention period will remain on hold until the court returns the documents to the investigators.
Yoon did not attend the court's closed-door hearing, held as part of the review, citing security issues. Instead, his lawyers appeared on his behalf.
The CIO is expected to file for another court warrant on Friday to officially arrest him to further investigate Yoon in custody.