After a hard-fought election campaign, Mr Yoon was declared winner as rival Lee Jae-myung from the incumbent Democratic party conceded defeat, with Mr Yoon gaining 48.56 per cent of the vote against Lee's 47.83 per cent, according to South Korea's National Election Commission.
Mr Yoon's victory marks a stunning turnaround for the main conservative bloc, now known as the People Power Party, which has regrouped since the 2017 election after the impeachment and ouster of then President Park Geun-hye.
More than 77 per cent of South Korea's 44 million eligible voters cast ballots to pick their next leader, despite a record surge in new Covid-19 cases this week
A political novice and avowed anti-feminist, Mr Yoom promised a more hawkish policy on the nuclear-armed North, with Pyongyang's record-breaking blitz of weapons testing this year, including a launch just days before the election.
“But the door to dialogue is always open,” he told supporters after visiting the national cemetery in Seoul.
He also vowed to forge even closer ties with the United States, in the face of increased missile activity by North Korea and competition with China, which is the South's largest trading partner.
The White House congratulated Mr Yoon, saying President Joe Biden looked forward to working closely with him to bolster the alliance.
Mr Yoon and Mr Biden spoke by telephone on Thursday, the White House said.
Japanese Prime Minister Fumio Kishida welcomed Mr Yoon's win, and said he hoped to work closely with him to rebuild healthier ties with its neighbour amid tensions over historic and economic disputes dating to Japan's 1910-1945 occupation of Korea.
Rival blames 'shortcomings'
Mr Yoon said he would work with opposition parties to heal polarised politics and foster unity.
“Our competition is over for now,” he said in an acceptance speech, thanking and consoling Mr Lee and other rivals. “We have to join hands and unite into one for the people and the country.”
Mr Lee had conceded defeat and congratulated his opponent.
“I did my best, but failed to live up to your expectations,” he told a news conference, blaming his “shortcomings” .
Mr Yoon has pledged to stamp out graft, foster justice and create a more level economic playing field, while seeking a “reset” with China and a tougher stance towards reclusive North Korea.
He faces the challenge of uniting a country of 52 million riven by gender and generational divisions, growing inequality and surging home prices.
“Real estate prices, housing policy, jobs, and tax policies will top his domestic agenda,” Duyeon Kim, a Seoul-based expert with the Center for a New American Security, told AFP.
Outgoing President Moon Jae-in's Democratic Party has a majority in the country's parliament, which could pose a challenge to Mr Yoon, who has no legislative experience.
“After a divided electorate has produced a divided government, Seoul may struggle to pursue policies of reform rather than politics of retribution,” said Leif-Eric Easley, a professor of international studies at Ewha Womans University in Seoul,
“His lack of experience on any real policymaking is a serious concern,” Karl Friedhoff of the Chicago Council on Global Affairs told AFP.
Fear of abolishing gender equality
During his campaign trail, Mr Yoon specifically courted disgruntled young male voters, with a promise to abolish the gender equality ministry, on the basis that South Korean women do not suffer from “systemic gender discrimination”, despite evidence to the contrary.
“My heart is very heavy and desperate,” Kim Ju-hee, a women's rights activist told AFP.
Mr Yoon's win has “set a precedent where a president-elect can openly ridicule women,” she added.
Exit polls showed Yoon getting 58.7 per cent support from men in their 20s, compared to Lee at 36.3 per cent. But for women in their 20s, Mr Lee received 58 per cent to Mr Yoon's 33.8.
“The widespread support Yoon enjoys from young men is, frankly, absolutely terrifying from a woman's point of view,” academic and female voter Keung Yoon Bae told AFP.
Mr Yoon will formally succeed Mr Moon in May. The incumbent remains popular, despite not achieving a promised peace deal with North Korea.