Meanwhile, Yoon’s People Power Party, plus other conservative coalitions, secured just under 110 seats.

Not all legislators represent specific locales. Forty-six are elected as proportional representatives based on the total vote by party. Turnout had been the highest in more than three decades, with roughly two-thirds of South Korea’s 44.3 million voters casting a ballot.

Two years ago, Kim Sun-woo, a 36-year-old office worker in Seoul, had supported Yoon, a political outsider and career prosecutor, in a historically close presidential race. Now, he is disappointed that many of Yoon’s election promises have failed to materialize. He backed the left-leaning party instead. 

“Like many people, I voted based on the urge to send a message to the current administration,” Kim said.

The race also featured, for the first time, a bigger swath of eligible older voters than younger ones, prompting some South Koreans like 28-year-old Lee Jin-seo, who generally doesn’t have much interest in politics, to turn out. “I think more of us need to be at voting booths if we want politicians to care about us,” Lee said of younger voters.

By law, the 63-year-old Yoon can’t run for re-election. His five-year term ends in 2027.

On Thursday, Yoon said he would humbly accept the election defeat, vowing to reform state affairs and stabilize the economy, according to South Korea’s presidential office. The ruling party chairman, Han Dong-hoon, said he would resign.

Yoon’s approval ratings have largely remained in the mid-30s over the past year. About a year ago, he traveled to Washington for a state visit at the White House, meeting President Biden and belting out parts of Don McLean’s “American Pie.” Back home, it was a less momentous story: South Korea’s economy grew last year at a far lower rate than other wealthy democracies, and inflation that had been tamed locally over the decades began to spiral upward. 

As a presidential candidate, Yoon favored throwing uppercuts at rallies and touted justice as a prosecutor who rooted out corruption. But in office, Yoon’s legal scrutiny of opposition-party figures came off as politically motivated, while he blocked parliamentary attempts to investigate his wife, first lady Kim Keon-hee, who had accepted a $2,200 Dior bag as a gift.

Wednesday’s results suggest Yoon—who dramatically strengthened ties with the U.S. and Japan and took a tougher line with North Korea—will face major difficulties in his final three years of office. At home, Yoon faces hurdles to pursue a domestic agenda, with the National Assembly controlled again by the opposition Democratic Party. 

Outside the country, the voter rejection of Yoon creates questions as to whether South Korea’s conservatives will be able to hold on to power during the next presidential election. If those doubts persist, friends—and even foes—of Seoul might operate with the assumption that Yoon’s foreign-policy direction could have an expiration date.

Yoon has steered South Korea more toward the global stage, backing the Western-led liberal order, contributing artillery shells to support Ukraine and attending North Atlantic Treaty Organization summits. But a protracted political gridlock, as domestic issues go unresolved, brings some risk to Yoon’s foreign-policy mission, said Andrew Yeo, a senior fellow who focuses on Korean issues at the Brookings Institution, a Washington D.C.-based think tank. 

“It would be a loss for the international community if South Korea turns inward because they have these roiling problems at home,” Yeo said.

Unlike his left-leaning predecessor, Moon Jae-in, Yoon has adopted a more confrontational stance with Pyongyang, believing peace is attained through strength. North Korean leader Kim Jong Un early this year declared the South as his country’s No. 1 enemy. During a Wednesday visit to a top military university, Kim implored students to be “more thoroughly prepared for a war than ever before,” state media reported. 

In his remaining years in office, Yoon is likely to keep the focus on international affairs, said Joan Cho, an East Asian studies and government professor at Wesleyan University. “Yoon’s achievements have mostly been in foreign policy—intensifying economic links with the U.S. and improving bilateral and trilateral relations with Japan,” Cho said. 

The outcome hands a major victory to South Korea’s opposition party, and its leader Lee Jae-myung, the man who lost by a razor-thin margin to Yoon in the 2022 presidential election. Lee, who is 60, was stabbed in the neck in January and required emergency surgery. The alleged assailant told police he resorted to violence over fears that Lee and his party would storm to victories for the legislation, and later the country’s presidency. 

“The election was an assessment of Yoon’s presidency,” said Duyeon Kim, an adjunct senior fellow at the Center for a New American Security, a Washington D.C.-based think tank.

With a more than three-fifths legislative majority, South Korea’s left-leaning coalition can fast track legislation and thwart Yoon’s domestic agenda. But the outcome leaves the opposition party short of a two-thirds bloc that could override Yoon’s presidential vetoes or move for impeachment.

Kim Soo-young, a 43-year-old homemaker, said it was difficult to keep track of all the minor feuds between the two major parties. “I feel like the elections were all about attacking the other party rather than policies,” she said. 

Write to Timothy W. Martin at Timothy.Martin@wsj.com and Dasl Yoon at dasl.yoon@wsj.com