It was a scene of chaos in Parliament as the vote took place on Friday.
Lawmakers from the ruling Yun and Han Party of Power (PPP) protested after National Assembly Speaker Woo Wonshik announced that only 151 votes would be needed to pass the impeachment bill.
This meant that, unlike the 200 votes needed to impeach Yun, no votes from ruling lawmakers would be needed to impeach Khan in parliament this time.
Deputies from the ruling party gathered in the middle of the voting hall and chanted “invalid!” and “abuse of power!” in response and called on the speaker to resign. Most of them boycotted the vote.
The opposition first filed an impeachment motion against Khan on Thursday after he blocked the appointment of three judges chosen by parliament to oversee Yun’s case.
The Constitutional Court of Korea normally consists of nine members. At least six justices must uphold Yun’s impeachment for the ruling to stand.
Currently, there are only six justices on the bench, meaning that one recusal would save Yoon from removal.
The opposition hoped that the three additional nominations would help increase Yun’s chances of impeachment.
Finance Minister Choi Sang Mok is set to replace Khan as acting president.
Khan’s removal is likely to add to the political gridlock and uncertainty the country is currently grappling with.