The country has been plunged into political chaos since last month, with Yoon defiantly holed up in the presidential residence, surrounded by hundreds of loyal security officers who have so far resisted efforts by prosecutors to arrest him.
Thousands of protesters, both for and against Yoon, gathered in front of the residence and along major roads in Seoul on Saturday -- either demanding his arrest or calling for his impeachment to be declared invalid.
Supporter Kim Chul-hong, 60, said Yoon's arrest could undermine South Korea's security alliance with the US and Japan.
"Protecting President Yoon means safeguarding our country's security against threats from North Korea," he told AFP.
Members of the Korean Confederation of Trade Unions, South Korea's largest umbrella union, attempted to march to Yoon's residence to protest against him, but were blocked by police.
It said two of its members were arrested, and several others were injured in clashes.
Yoon faces criminal charges of insurrection, one of a few crimes not subject to presidential immunity, meaning he could be sentenced to prison or, at worst, the death penalty.
If the warrant is executed, Yoon would become the first sitting South Korean president to be arrested.
Arrest showdown
Investigators have asked Finance Minister Choi Sang-mok, who was installed as acting president a week ago, to back the warrant by ordering the presidential security service to cooperate.
The Service said two top officials from the had refused a police request Saturday for questioning, citing the "serious nature" of protecting him.
In scenes of high drama on Friday, Yoon's guards and military troops shielded him from investigators who eventually called off the arrest attempt citing safety concerns.
The showdown -- which reportedly included shoving but no shots fired -- left the warrant in limbo, with the court order set to expire on Monday.
CIO officials could make another bid to arrest him before then.
But if the warrant lapses, they may apply for another.
The Constitutional Court slated January 14 for the start of Yoon's impeachment trial, which if he does not attend would continue in his absence.
Former presidents Roh Moo-hyun and Park Geun-hye never appeared for their impeachment trials.
Yoon's lawyers decried Friday's arrest attempt as "unlawful and invalid", and vowed to take legal action.
Experts said investigators could wait for greater legal justification before attempting to arrest the suspended president again.
"It may be challenging to carry out the arrest until the Constitutional Court rules on the impeachment motion and strips him of the presidential title," Chae Jin-won of Humanitas College at Kyung Hee University told AFP.
'Stable path'
Yoon has remained defiant and told his right-wing supporters this week he would fight "to the very end" for his political survival.
By the time investigators arrived to arrest Yoon, he had layered his presidential compound with hundreds of security forces.
Around 20 investigators and 80 police officers were heavily outnumbered by around 200 soldiers and security personnel linking arms to block their way.
The weeks of political turmoil have threatened the country's stability.
South Korea's key security ally, the United States, called for the political elite to work towards a "stable path" forward.
Outgoing US Secretary of State Antony Blinken is scheduled to hold talks in Seoul on Monday, with one eye on US-South Korea relations and another on nuclear-armed North Korea.
