Conservatives worry that a victory by Moon Jae-in might benefit North Korea and estrange South Korea and its most important ally, the United States.
Moon was the clear favorite as conservative forces struggled to regroup after the huge corruption scandal ended Park Geun-hye's presidency.
"I gave all my body and soul (to the election) to the very end. My party and I invested all our efforts with a sense of desperation, but we also felt a great desire by people to build a country we can be proud of again," Moon, 64, told reporters after casting his ballot.
His victory would end a near-decade of conservative leadership by Park and Lee Myung-bak. Moon was chief of staff for the last liberal President Roh Moo-hyun, who sought closer ties with North Korea by setting up large-scale aid shipments to the North and by working on now-stalled joint economic projects.
Outspoken conservative Hong Joon-pyo, the candidate from Park's Liberty Korea Party, described the election as a war between ideologies and accused Moon of being aligned with North Korea.
Hong has pitched himself as a "strongman" who can hold his own against other "nationalist" leaders in Washington, Tokyo and Beijing. He also calls for the United States to bring back tactical nuclear weapons to South Korea after withdrawing them in the 1990s.
The polls have shown Hong and centrist Ahn Cheol-soo running even.
Voting stations are set to close at 8 pm and South Korean TV stations plan to release the results of their joint exit polls soon after the vote ends and are expected to predict a winner before midnight.
The winner will be sworn in after the National Election Commission ends the vote count and confirms the result tomorrow.
Because the vote is a special election, the new president will forgo the usual two-month transition and will serve one full, five-year term rather than only completing Park's original term, which was to have ended in February 2018.
Some voters were eager to end the long conservative rule, which they think failed the economy and undermined democracy before the corruption scandal toppled Park.
Others were more concerned about the growing threats posed by North Korea's nuclear weapons and missiles and fears over Seoul losing its voice in international efforts to deal with its belligerent rival.
"We need a leader who could protect national interests and hold his ground against the surrounding global powers of the United States, China and Japan," said Kim Hyeong-seok, a 67-year-old who said he voted for Hong. "This is not the time to keep our eyes just on domestic issues we need to think about the nation's long-term future and peace.
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