A two-thirds majority of the National Assembly was required to pass the impeachment bill, which means that at least eight PPP MPs must vote for it.
However, all but three left the hall earlier on Saturday.
One of those who remained, Cho Kyung-tae, credited Yoon’s apology for the martial law order on Saturday morning – after three days out of the spotlight – as influencing his decision not to support impeachment this time.
“The president’s apology and his willingness to resign early, as well as the delegation of all political tasks to the party, influenced my decision,” he told the BBC ahead of the vote.
Cho said he believed impeachment would hand the presidency to Democratic Party of Korea (DPK) leader Lee Jae-myung.
He added that Yun’s “irrational and absurd decision” to declare martial law “overshadowed” what he called “many extreme actions” by the DPK during its time in power.
After Saturday’s vote, Lee insisted that his party would “not give up” on its efforts to impeach Yun, who he said was the “worst risk” to South Korea.
“We will definitely get this country back to normal by Christmas and the end of the year,” he told a crowd gathered outside parliament in the capital, Seoul.