Mr Yoon, a political novice, edged out a victory over the Democratic Party's Lee Jae-myung based on promises to tackle class inequality.
He called his win a "victory of the great South Korean people".
But the result was one of the closest in history - with the final count separated by less than 1%.
Early on Thursday morning, Mr Yoon told supporters at his victory ceremony he would "pay attention to people's livelihoods, provide warm welfare services to the needy, and make utmost efforts so that our country serves as a proud, responsible member of the international community and the free world".
Both presidential candidates were viewed as widely unpopular throughout the campaign. Analysts said voters appeared so disenchanted by the frontrunners that local media dubbed the vote "election of the unfavourables".
Still, Wednesday's election saw a high turn out, with 77% of eligible voters casting a ballot.
Top of voters' concerns were skyrocketing house prices, stagnant economic growth, stubborn youth unemployment and gender inequality.
Mr Yoon had also made abolishing the Ministry of Gender Equality and Family a central pledge of his campaign.
The ministry largely provides family-based services, education, and social welfare for children and spends around 0.2% of the nation's annual budget - less than 3% of which goes towards the promotion of equality for women.
During his campaign Mr Yoon had also leant heavily into a support base of young men, some of whom declared that there was no systemic gender discrimination in South Korea.
Demographic breakdowns of the vote showed that many had voted for the third female candidate Sim Sang-jung who'd advocated for gender equality, the BBC's Laura Bicker reports.
In the foreign policy space, Yoon has promised a tougher "reset" on relations with China and North Korea and indications of closer ties with the US.
The White House has already sent its congratulations to Mr Yoon, saying US President Joe Biden is looking forward to further expanding the two countries ties
Yoon will become president but with a Democratic Party-majority in the single-house National Assembly. The incumbent Moon Jae-in of the Democratic Party had to step down due to constitutional five-year limits of the presidential term.
