Crowds gathered at Mr. Magufuli’s official residence on Thursday, carrying wreaths and party flags and singing religious songs on the first of 14 official days of mourning. Tanzania’s government has made no further statement since Vice President Samia Suluhu Hassan announced late Wednesday on state television that Mr. Magufuli had died from a heart condition that had plagued him for a decade.

Opposition leaders and diplomats in Dar es Salaam, Tanzania’s largest city, had said for days that the 61-year-old Magufuli disappeared from public view 12 days ago because he had contracted the coronavirus after the sudden deaths of five members of his cabinet.

Ms. Hassan, now president-elect, would be Tanzania’s first female president.

The confirmation of Mr. Magufuli’s death extends the paradox of the coronavirus pandemic in Africa, a continent that has registered fewer cases compared with elsewhere in the world but where several prominent leaders have died unexpectedly from coronavirus-like symptoms.

Africa’s 54 nations, with a population of about 1.3 billion, have reported only four million cases and around 100,000 deaths, far behind the U.S. tally of 29.6 million cases and 538,000 deaths among a population of about 328 million. But the continent has lost more senior leaders from the coronavirus-related complications than anywhere else in the world.

In neighboring Burundi, longtime leader Pierre Nkurunziza unexpectedly died with coronavirus-like symptoms last year while his wife was airlifted to a hospital in Nairobi to be treated for coronavirus. The vice president of Tanzania’s semiautonomous archipelago of Zanzibar, Seif Sharif Hamad, died last month days after his party announced he had tested positive for the virus. Uganda’s deputy prime minister and Eswatini’s prime minister also died from the virus last year.

Despite the rise in high-profile cases, Mr. Magufuli’s death comes at a moment when his brand of Covid-skepticism is flourishing in the region’s most impoverished states.

Burundi’s health minister said last month that his country didn’t need Covid-19 vaccines, since the majority of patients were recovering. Eritrea and Madagascar have also declined the vaccines, with Madagascar President Andry Rajoelina promoting a locally produced herbal remedy.

Vaccine skepticism is aggravating Africa’s yawning supply gap, with less than one dose for 100 people by the end of February, compared with 31 doses for 100 people in the U.K. and 22 per 100 the U.S., according to data compiled by the University of Oxford.

Diplomats and policy analysts in Tanzania say the key question for the gold-producing nation is whether the ruling Chama Cha Mapinduzi party can manage a smooth transition to Ms. Hassan.

The populist Mr. Magufuli, known as “the Bulldozer” for his no-nonsense approach to corruption and poverty reduction, centralized power around his personal authority. He comfortably won October elections, with Ms. Hassan playing a minor role as his running mate.

“We don’t expect Ms. Suhulu [Hassan] to immediately reverse the government’s response and impose strict Covid-19 restrictions but she will likely do so gradually in coming months, said Zaynab Mohamed, a Tanzanian analyst with NKC African Economics. “If she makes drastic changes quickly, it could negatively affect her.”

The ruling party has said it would not contest Ms. Hassan’s swearing-in as president in the coming days but opposition leaders have called for her immediate swearing in, warning that the constitution doesn’t provide for a continued power vacuum.

In recent weeks, Mr. Magufuli had begun to belatedly institute public-health measures to contain the disease, including the wearing of masks, following a spate of high-profile deaths. But the country continued to refuse to share tallies of coronavirus cases with the World Health Organization, which it stopped providing almost a year ago.

Despite his coronavirus stance and a mounting clampdown on rights and freedoms that made him an international pariah, Mr. Magufuli remained popular at home, particularly in rural communities that benefited from one of Africa’s highest growth rates in recent years. In Dar es Salaam, Tanzania’s commercial capital, scores of residents huddled inside cafes and restaurants and outside on street corners to watch news about his death. Some wept as they watched the news bulletins.

Some analysts said Ms. Hassan, who has less of a political constituency, may find it tougher to continue Mr. Magufuli’s confrontational stance against international mining companies.

“Investors will be watching closely for signs Magufuli’s replacement will either stick to or diverge from the former president’s resource-nationalist path,” said Ed Hobey-Hamsher, an analyst with risk-analysis firm Verisk Maplecroft.

Barrick Gold Corp.’s chief executive, Mark Bristow, who tussled with Mr. Magufuli for years over a high-profile tax spat in 2017 that resulted in the company paying $300 million, expressed his condolences to the Tanzanian people, describing the late leader as “a visionary statesman.”

Mr. Magufuli’s contrarian approach on the pandemic has particularly irked Washington, Tanzania’s top health and security donor that has invested around $4.9 billion in its health sector over the past two decades.

Tanzanian authorities closed down a TV station last summer for reporting on a U.S. Embassy statement that warned of rising coronavirus cases across the country. Weeks later, Mr. Magufuli accused the embassy of exaggerating the health crisis, and warned citizens against accepting U.S. donations of items such as masks and other medical supplies.

As Mr. Magufuli insisted that his country was coronavirus-free, the U.S. countered him several times, straining ties. Days before the death of the vice president of Zanzibar, the U.S. Embassy again warned of a significant increase of coronavirus cases in Tanzania. Days later, Mr. Magufuli’s chief secretary died unexpectedly, drawing panic within government circles.

On Thursday, the U.S. State Department expressed condolences following Mr. Magufuli’s death and pledged to support Tanzania in combating the pandemic.

Write to Nicholas Bariyo at nicholas.bariyo@wsj.com