Yoon last week became the first sitting South Korean president to be arrested as he faces allegations of insurrection related to his stunning Dec. 3 declaration of martial law that has plunged the country into political turmoil.
Shortly after the court's decision was announced around 3am (1800 GMT) on Sunday, his supporters swarmed the building, overwhelming riot police trying to keep them at bay.
Footage showed protesters blasting fire extinguishers at officers guarding the front entrance, before they flooded inside, destroying furniture and computers.
Police arrested 46 protesters and restored order a few hours later, local media reported, citing police.
With a requirement either to petition toextend Yoon's detention or free the impeached president within 48 hours, South Korean investigators asked a Seoul court on Friday to hold him for longer after he refused to be questioned.
After a 5-hour hearing on Saturday, which Yoon attended, the Seoul Western District Court opted to grant the investigators' request due to "concern that the suspect may destroy evidence," the court said in a statement.
Under the new warrant, Yoon can be detained for up to 20 days. South Korean regulations require a suspect detained under a warrant to undergo a physical exam, have a mugshot taken and wear a prison uniform.
The leader is expected to continue to be held in a solitary cell at the Seoul Detention Centre.
The CIO said in a statement it will investigate Yoon in accordance with the law and procedure.
Seok Dong-hyeon, one of Yoon's lawyers, said the court's decision was "really hard to understand" but asked for calm.
"Such expressions of anger are understandable, but if they go too far and continue to be violent, they could be caught up in targeted attacks or counter-attacks by leftist forces," he said. "We need to stay calm," he said in a Facebook post.
Yoon's ruling People Power Party called the court's decision a "great pity".
"There's a question whether repercussions of detaining a sitting president were sufficiently considered," the party said in a statement.
The major opposition Democratic Party called the court's approval on the warrant a "cornerstone for rebuilding the collapsed constitutional order".
Support for the PPP collapsed after his martial law declaration, which he rescinded hours later in the face of a unanimous vote in parliament rejecting it. Lawmakers impeached Yoon on Dec. 14, suspending his presidential powers.
But in the turmoil since - in which the opposition-majority parliament also impeached his first replacement and investigators botched an initial attempt to arrest Yoon - the PPP's support has sharply rebounded.
His party has edged ahead of the opposition Democratic Party in support - 39% to 36% - for the first time since August, a Gallup Korea poll showed on Friday.
Denying the allegations that he masterminded insurrection, Yoon has so far stonewalled efforts by the CIO to interrogate him, refusing to attend questioning.
His lawyers have argued the arrest is illegal because the warrant was issued in the wrong jurisdiction and the investigating team had no mandate for their probe.
Insurrection, the crime that Yoon may be charged with, is one of the few that a South Korean president does not have immunity from and is technically punishable by death. South Korea, however, has not executed anyone in nearly 30 years.
Separate to the criminal probe that sparked Sunday's chaos, the Constitutional Court is deliberating over whether to uphold the impeachment and permanently remove him or restore his powers.
