Early on Tuesday morning, a rolling ballot count by an election commission-accredited watchdog showed Duterte had almost 39 percent of votes cast. He was more than 5 million votes ahead of his nearest rival with 90 percent of votes counted.
Grace Poe, a popular senator, won more than a fifth of the votes counted but conceded defeat to Duterte and said his lead reflected the will of the people.
Duterte's incendiary rhetoric and advocacy of extrajudicial killings to stamp out crime and drugs have alarmed many who hear echoes of the Southeast Asian country's authoritarian past.
The 71-year-old's truculent defiance of political tradition has drawn comparisons with U.S. Republican presidential candidate Donald Trump, as have his references to his libido.
Duterte made a succession of winding, bellicose and at times comical remarks on television as the votes were being counted, venting over corruption and bad governance and telling anecdotes from his 22 years as mayor of Davao city.
He said corrupt officials should "retire, or die" and reiterated his support for police to use of deadly force against criminals.
"If they put up a good fight and refuse to surrender and if you feel your life is in jeopardy, shoot. You have my authority," he told reporters in Davao, wearing a checked shirt and slouched in a chair.
His man-of-the-people demeanor tapped into popular disgust with the political establishment over its failure to tackle poverty and inequality despite several uninterrupted years of robust economic growth.
The election numbers reported by the Parish Pastoral Council for Responsible Voting (PPCRV) had, by 5:30 am (0930 GMT), accounted for about 90 percent of the 54 million registered Filipino voters.
Duterte had 14.9 million votes, with the government's candidate Manuel Roxas second with 8.9 million, followed by Poe with 8.3 million votes.
The PPCRV count is not official but Poe's decision to concede defeat added weight to his presumed victory.
Duterte had earlier talked of making peace with his rivals after a "virulent" campaign, during which Poe called him "an "executioner". She later said she was willing to bury the hatchet.
"I promise to cooperate with the healing process," she told reporters. "Duterte has a mandate. Let's give him a chance."
In an early indication of his unorthodoxy, Duterte told reporters that if he became president he would seek multilateral talks to resolve disputes over the South China Sea.
The outgoing administration of President Benigno Aquino has asked a court of arbitration in The Hague to recognize its right to exploit waters in the South China Sea, a case it hoped could bolster claims by other countries against China in the resource-rich waters.
Duterte said negotiations should include Japan, Australia and the United States, which is traditionally the region's dominant security player and contests China's development of islands and rocky outcrops in the sea.
Asked about U.S. support for Duerte's proposal, Anna Richey-Allen, a spokeswoman for the State Department's East Asia Bureau, said: "The United States has consistently expressed support for nations to exercise peaceful means to resolve territorial or maritime disputes without the use or threat of force, intimidation or coercion, and in a manner consistent with international law."
POLICY UNCERTAINTY AHEAD
At least 11 people were killed in violence before voting started, but otherwise the election was mostly smooth. Voters also cast ballots for the vice president, 300 lawmakers and about 18,000 local government officials.
"Bongbong" Marcos Jr., the son and namesake of late dictator Ferdinand Marcos, was neck and neck with Congresswoman Leni Robredo in the vice president race.
Duterte's entertaining speeches, often loaded with profanities, have shed little light on his policies beyond going after gangsters and drug pushers.
He has been vague on what he would do to spur an economy that has averaged growth at around 6 percent under Aquino.
In a report on Monday, ratings agency S&P Global said a Duterte presidency would create uncertainty, especially if he picks fights with the political elite.
"He could take some time getting used to the many compromises required in the national leadership position," it said.
One indication of that came on Monday as Duterte told reporters he planned to loosen restrictions on foreign ownership of companies across all industries, which could meet with resistance from protectionist forces.
One of Duterte's economic advisers told Reuters spending on education would be lifted to benefit "disadvantaged regions" and agriculture and rural development will be prioritized to spread wealth more evenly across the country.
"Everything seems to be in imperial Manila. He wants to give more attention to the lagging, the backward regions," said Ernesto Pernia, professor emeritus of economics at the University of the Philippines.
Pernia said the pursuit of tax evaders and corrupt officials should bolster government revenues to fund extra spending.