Under the constitution Prime Minister Han Duck-soo, who was appointed by Yoon, becomes acting president, while Yoon remains in office but with his presidential powers suspended.
Han said he would make his utmost efforts to ensure stability after Yoon's impeachment. "I will give all my strength and efforts to stabilise the government," Han told reporters.
Yoon is the second conservative president in a row to be impeached in South Korea. Park Geun-hye was removed from office in 2017. Yoon survived a first impeachment vote last weekend, when his party largely boycotted the vote, depriving parliament of a quorum.
Protesters backing Yoon's impeachment leapt for joy near parliament at the news and waved colourful LED sticks as music pumped out. By contrast, a rally of Yoon supporters quickly emptied following the news.
The impeachment motion was carried after at least 12 members of Yoon's People Power Party joined the opposition parties, which control 192 seats in the 300-member national assembly, clearing the two-thirds threshold needed for impeachment.
The number of lawmakers supporting impeachment was 204, with 85 against, three abstentions and eight invalid ballots.
The Constitutional Court will decide whether to remove Yoon sometime in the next six months. If he is removed from office, a snap election will be called.
Yoon shocked the nation late on December 3 when he gave the military sweeping emergency powers to root out what he called "anti-state forces" and overcome obstructionist political opponents.
He rescinded the declaration barely six hours later, after parliament defied troops and police to vote against the decree. But it plunged the country into a constitutional crisis and triggered widespread calls for him to step down on the grounds that he had broken the law.
Yoon later apologised to the nation but defended his decision and resisted calls to resign.
Opposition parties launched the fresh impeachment vote, with large demonstrations supporting impeachment.
Yoon is also under criminal investigation for alleged insurrection over the martial law declaration and authorities have banned him from travelling overseas.
In a defiant speech on Thursday, Yoon vowed to "fight to the end", defending his martial law decree as necessary to overcome political deadlock and protect the country from domestic politicians who he said were undermining democracy.
