The 64-year-old leader said he agreed to appear before the Corruption Investigation Office for high ranking officials (CIO) to avoid bloodshed.
In a three-minute video message, Yoon said he would comply with the investigation against him even though he was against it.
He has consistently maintained that the warrant for his arrest is not legally valid.
Yoon said he witnessed how authorities “invaded” his home’s security perimeter with fire equipment.
“I decided to appear before the CIO, even though it is an illegal investigation, in order to prevent any unsavoury bloodshed,” he said.
Tense scenes unfolded at dawn as the arrest team moved past barricades. Throngs of Yoon supporters chanted “end the impeachment” while a separate group of critics shouted “arrest him”.
More than 1,000 officers were part of Wednesday’s operation, which marked the second time officers had tried to arrest him.
The CIO which is investigating Yoon, previously attempted to arrest him on 3 January but they were blocked by buses and barbed wire.
They had obtained the warrant after he ignored multiple summonses to appear for questioning.
On Wednesday, they came with tools to overcome the obstacles, climbing over the parked vehicles with ladders and cutting through barbed wire fences.
Some managed to access the presidential residence through a nearby hiking trail, local media reported.
Yoon’s People Power Party decried his arrest as “illegal”, with floor leader Kweon Seong-dong describing Wednesday’s events as “regretful”.
On the other hand, the floor leader of the opposition Democratic Party, Park Chan-dae, said Yoon’s arrest showed that “justice in South Korea is alive”.
This arrest “is the first step toward restoring constitutional order, democracy and the rule of law,” he said during a party meeting.
The country is currently being led by Finance Minister Choi Sang-mok as acting president. He was thrust into power after the first acting president, Han Duck-soo, was also impeached by opposition majority parliament.
Yoon is expected to be detained at the Seoul Detention Centre in Uiwang, Gyeonggi Province, approximately 5km (3 mi) from the CIO’s office.
If a court doesn’t issue a detention warrant within 48 hours of Yoon’s arrest, however, he will be released, and free to return to the presidential residence.
Yoon has been questioned by investigators but has invoked the right to remain silent.
While the arrest of a sitting president is remarkable for South Korean politics, the country’s political crisis is far from over. It is just another phase in an unfolding political drama.
The crowds outside Yoon’s house on Wednesday morning underscored the deep divisions in the country.
The anti-Yoon crowd cheered, clapped and blasted out a “congratulations and celebrations” song at the announcement of his arrest.
The atmosphere is completely different on the other side.
“We are very upset and angry – the rule of law has broken down,” a Yoon supporter told the BBC.
The standoff also pitted two branches of executive power against each other: law enforcement officers, armed with a legal arrest warrant and presidential security staff, who said they were duty bound to protect the suspended president.
Even before his martial law declaration, Yoon had been reduced to a lame duck leader as the opposition party held the majority in parliament.
He has also faced controversy over his wife for receiving a Dior bag as a gift.
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