In an election upset in Iran, the reformist candidate who advocated moderate policies at home and improved relations with the West won the presidential runoff against his hard-line rival, the interior ministry said on Saturday.

The reformist candidate, Masoud Pezeshkian, 69, a cardiac surgeon, got 16.3 million votes to defeat Saeed Jalili, with 13.5 million votes. The result delivered a blow to the conservative faction and was a major victory for the reformist camp, which had been sidelined from politics for the past few years.

After polls closed at midnight, turnout stood at about 50 percent, roughly 10 percentage points higher than in the first round with about 30.5 million ballots cast, according to the interior ministry.

The first round had a record low turnout because many Iranians boycotted in protest. But the prospect of a hard-line administration that would double down on strict social rules, including enforcing mandatory hijabs for women, and remain defiant in negotiations to lift international economic sanctions, seemed to have spurred Iranians to turn out.

Mr. Pezeshkian’s supporters took to the streets before dawn on Saturday, according to video footage on social media and his campaign, honking horns, dancing and cheering outside his campaign offices in many cities, including his hometown, Tabriz, when initial results showed he was leading. They also took to social media to congratulate Iranians for turning up at polls to “save Iran,” a campaign slogan of Mr. Pezeshkian’s.

“The end of the rule of minority over majority,” Ali Akbar Behmanesh, a reformist politician and head of Mr. Pezeshkian’s campaign in the province of Mazandaran, said on X. “Congratulations for the victory of wisdom over ignorance.”

Some conservative supporters of Mr. Jalili said on social media that regardless of who won, the turnout was a victory for the Islamic Republic and they hoped the new administration would work to bridge divisions among political factions.

While Iran’s supreme leader, Ayatollah Ali Khamenei, wields the most power in government, analysts said the president could set domestic policies and shape foreign policy.

“A reform-minded president, despite all the limitations and failures of the past, is still meaningfully better — in some significant way it would put some constraint on the authoritarianism of the Islamic Republic,” said Nader Hashemi, a professor of Middle Eastern studies at George Washington University.

The special election was held because President Ebrahim Raisi was killed in a helicopter crash in May. Mr. Pezeshkian’s new term will last four years.

Elections in Iran are not free or fair by Western standards, and the selection of candidates is tightly vetted by the Guardian Council, an appointed committee of 12, with six clerics and six jurists. But the government has long viewed voter turnout as a sign of legitimacy.

The two candidates in the runoff, from opposite ends of Iran’s constrained political spectrum, represented different visions for Iran, with consequences for domestic and regional politics.

In the days before the election, Mr. Pezeshkian’s campaign rallies attracted larger and younger crowds. Prominent politicians like Mohammad Javad Zarif, a former foreign minister, campaigned for him and said the choice was between “day and night.”

The message that voters should turn up out of fear of Mr. Jalili appeared to have resonated.

“I’m going to vote, because if I don’t vote, the Islamic Republic won’t be toppled,” Ghazal, a 24-year-old fashion designer in Tehran, the capital, said in a telephone interview. Like others interviewed, she asked to be identified only by her first name for fear of drawing the government’s attention.

Sedigheh, a 41-year-old pediatrician in Tehran, also abandoned her boycott and voted for Mr. Pezeshkian on Friday, even though she said by telephone that she had no hope that any president could bring about meaningful changes that people demanded.

“I voted, because I think we need small and incremental changes that make our lives a little better,” she said, “and if there is a president who can or wants to make those small changes, it’s enough for now.”

A veteran of the Iran-Iraq war, Mr. Pezeshkian served in Parliament for 16 years, including a stint as deputy Parliament speaker, and as health minister for four years. After his wife died in a car accident, he raised his children as a single father and has never remarried. That, and his identity as an Azeri, one of Iran’s ethnic minorities, endeared him to many voters. He campaigned with his daughter by his side at every rally and major speech.

Many conservatives crossed party lines and voted for Mr. Pezeshkian because, they said, Mr. Jalili was too extreme and would deepen tensions at home.

“Mr. Jalili cannot unite Iranians,” Saeed Hajati, a conservative who said he was voting for Mr. Pezeshkian while at a town-hall-style meeting on Thursday that was streamed on the Clubhouse app. “He will divide us more, and we need someone who can bridge these divisions.”

Mr. Pezeshkian campaigned on a promise to work with his rivals to solve Iran’s many challenges. In his last campaign video message, he told Iranians, “I am your voice, even the voice of the 60 percent whose voice is never heard and did not show up at the polls.” He added, “Iran is for everyone, for all Iranians.”

Mr. Jalili campaigned on the message that he would safeguard revolutionary ideals and remain defiant against challenges like sanctions and nuclear negotiations.

In the days before the vote, prominent politicians and clerics called Mr. Jalili “delusional,” compared him to the Taliban in Afghanistan and warned that his presidency would put the country on a collision course with the United States and Israel.

Reformists in Iran said that Mr. Pezeshkian’s election campaign was a boost for their political movement, which many inside and outside the country had written off after being marginalized in parliamentary elections and the last presidential election, in 2021. That year, competitive candidates were disqualified, while those who remained faced a disillusioned electorate.

“The reformist movement got a new lifeline in the country, and reformists came with all their force to support him,” Ali Asghar Shaerdoost, former member of Parliament from the reformist party, said in a live town-hall-style gathering streamed on Clubhouse from Tehran.

Many Iranians have called for an end to the Islamic Republic’s rule in waves of protests, including a 2022 uprising led by women in which crowds chanted, “Conservatives, reformists, the game is over.”

The government has brutally cracked down on dissent, killing more than 500 people and arresting tens of thousands. The widespread anger and loss of hope were reflected in the fact that half of eligible voters, about 61 million, sat out this election, saying that a vote for the government would be a betrayal of all victims.

Mahsa, a 34-year-old accountant in Isfahan, said by telephone that she refused to vote and was not buying the logic that she had to pick between bad and worse. “I see this election as government propaganda — a kind of ridiculous mask behind which everything is controlled by a dictator.”

A daunting list of challenges awaits the winner: an ailing economy debilitated by years of international economic sanctions, a frustrated electorate and geopolitical tripwires that have brought Iran to the brink of war twice this year. Many Iranians blame the government for wrecking the economy, limiting social freedoms and isolating the country.

During Mr. Raisi’s tenure, he oversaw a strategy of expanding Iran’s regional influence and strengthening ties with Russia and China. Iran-backed militant groups expanded their reach and gained more advanced weapons across the Middle East, and the country’s nuclear program advanced to weapons-threshold level in the aftermath of President Donald J. Trump’s withdrawing the United States from the nuclear deal in 2018.

As war rages between Israel and Hamas in Gaza, militant proxies backed by Iran have opened new fronts against Israel from Yemen to Lebanon. Those tensions took Iran to the brink of war with Israel in April and with the United States in February.

Leily Nikounazar and Alissa J. Rubin contributed reporting.