The impeachment bill needed a two-thirds majority in the National Assembly to pass, meaning at least eight PPP MPs would have to vote in favour.
However, all but three walked out of the chamber earlier on Saturday.
One of those who remained, Cho Kyung-tae, credited Yoon’s apology for the martial law decree on Saturday morning – after three days out of public view – as having influenced his decision not to back impeachment this time.
“The president’s apology and his willingness to step down early, as well as delegating all political agendas to the party, did have an impact on my decision,” he told the BBC ahead of the vote.
Cho said he believed impeachment would hand the presidency to the leader of the Democratic Party of Korea (DPK), Lee Jae-myung.
He added that Yoon’s “irrational and absurd decision” to declare martial law had “overshadowed” what he described as the DPK’s “many extreme actions” while in power.
DPK lawmaker Lee Unjoo told the BBC that she had cried when PPP politicians walked out.
“We did know there was a possibility they might boycott the vote, but we didn’t believe they would actually go through with it when tens of thousands of citizens were watching right outside,” she said.
Following Saturday’s vote, Lee insisted his party “will not give up” with its attempts to impeach Yoon, who he said had become “the worst risk” to South Korea.
“We will definitely return this country to normal by Christmas and the end of the year,” he told a crowd gathered outside the parliament in the capital, Seoul.