Han will be suspended from his duties as soon as he is officially notified by parliament.
The opposition first filed an impeachment motion against Han on Thursday after he blocked the appointment of three judges that parliament had chosen to oversee Yoon's case.
Korea's Constitutional Court is typically made up of a nine-member bench. At least six judges must uphold Yoon's impeachment in order for the decision to be upheld.
There are currently only six judges on the bench, meaning a single rejection would save Yoon from being removed.
The opposition had hoped the three additional nominees would help improve the odds of Yoon getting impeached.
This is the first time an acting president has been impeached since South Korea became a democracy.
Finance minister Choi Sang-mok is set to replace Han as acting president.
Like Yoon, Han's impeachment will need to be confirmed by the constitutional court, which has 180 days to rule on whether the impeachment should be upheld.
"I respect the decision of the National Assembly," Han said Friday, adding that he "will wait for the Constitutional Court's decision."
He also said that he would suspend his duties to "not add to the chaos".