For decades, sub-Saharan Africa was a singular focus of American foreign aid. The continent received over $8 billion a year, money that was used to feed starving children, supply lifesaving drugs and provide wartime humanitarian assistance.

In a few short weeks, President Trump and the South African-born billionaire Elon Musk have burned much of that work to the ground, vowing to completely gut the U.S. Agency for International Development.

“CLOSE IT DOWN!” Mr. Trump wrote on social media on Friday, accusing the agency of unspecified corruption and fraud.

A federal judge on Friday halted, for now, some elements of Mr. Trump’s attempt to shutter the agency. But the speed and shock of the administration’s actions have already led to confusion, fear and even paranoia at U.S.A.I.D. offices across Africa, a top recipient of agency funding. Workers were being fired or furloughed en masse.

As the true scale of the fallout comes into view, African governments are wondering how to fill gaping holes left in vital services, like health care and education, that until recent weeks were funded by the United States. Aid groups and United Nations bodies that feed the starving or house refugees have seen their budgets slashed in half, or worse.

By far the greatest price is being paid by ordinary Africans, millions of whom rely on American aid for their survival. But the consequences are also reverberating across an aid sector that, for better or worse, has been a pillar of Western engagement with Africa for over six decades. With the collapse of U.S.A.I.D., that entire model is badly shaken.

“This is dramatic and consequential, and it’s hard to imagine rowing it back,” said Murithi Mutiga, Africa program director at the International Crisis Group. Mr. Mutiga described the collapse of the agency as “part of the unraveling of the post Cold War order.”

“Once, the primacy of the West was assumed” in Africa, he said. “No more.”

Experts say the agency’s abrupt undoing will cost many lives by creating huge gaps in public services, especially in health care, where U.S.A.I.D. has poured much of its resources.

In Kenya alone, at least 40,000 health care workers will lose their jobs, U.S.A.I.D. officials say. On Friday, several U.N. agencies that depend on American funding began to furlough part of their staff. The United States also provides most of the funding for two large refugee camps in northern Kenya that house 700,000 people from at least 19 countries.

Ethiopia’s health ministry has fired 5,000 health care professionals who had been recruited under American funding, according to an official notification obtained by The New York Times.

“We are in disbelief,” said Medhanye Alem of the Center for Victims of Torture, which treats survivors of conflict-related trauma at nine centers in northern Ethiopia, all now closed.

Of over 10,000 U.S.A.I.D. employees worldwide, barely 300 will remain under changes conveyed to staff on Thursday night. Only 12 will remain in Africa.

The most pressing challenge for many governments is not to replace the American staff members or money, but to save American-built health systems that are rapidly crumbling to the ground, said Ken O. Opalo, a Kenyan political scientist at Georgetown University in Washington.

Kenya, for instance, has enough drugs to treat people with H.I.V. for over a year, Mr. Opalo said. “But the nurses and doctors to treat them are being let go, and the clinics are closing.”

Broader economic shocks are also likely in some of the world’s most fragile countries.

American aid accounts for 15 percent of economic output in South Sudan, 6 percent in Somalia and 4 percent in the Central African Republic, said Charlie Robertson, an economist who specializes in Africa. “We could see governance effectively cease in a few countries, unless others step up to replace the hole left by the U.S.,” he said.

Whether U.S.A.I.D. is truly dead may yet be determined by Congress and the U.S. courts, where supporters have filed a raft of legal challenges. But the Trump administration seems determined to move faster than its challengers.

As Mr. Musk and his team have commandeered the agency’s operations in Washington, shuttering its headquarters and sacking or suspending 94 percent of its staff, its vast aid machinery in Africa has shuddered to a halt.

In major hubs in Kenya, South Africa and Senegal, American aid officials were shocked to find themselves labeled “criminals” by Mr. Musk, then ordered to return to the United States, according to eight U.S.A.I.D. employees or contractors who all spoke on the condition of anonymity for fear of retaliation.

On Friday, the Trump administration gave all U.S.A.I.D. staff members 30 days to pack their bags and come home, causing turmoil among families now faced with the prospect of pulling children out of school on short notice. If the federal court that is now reviewing that directive does not overturn it, few will have jobs to return to.

Several U.S.A.I.D. officials noted that Google’s artificial intelligence system, Gemini, had been activated on their internal communications systems recently, and that internal video calls conducted on the Google platform were suddenly set to automatically record.

Officials said they worried that Mr. Musk’s team could use A.I. to monitor their conversations to ferret out dissenters, or to excerpt snippets of conversations that might be weaponized to discredit the agency.

Colleagues at the agency have turned to Signal, an encrypted messaging app, this week to share information unofficially. People are being driven by fear, one of them said.

In private, even senior U.S.A.I.D. officials agree that the agency needs an overhaul. In interviews, several recognized the need to streamline its bureaucracy, and even questioned an aid system that relies so heavily on American contractors and fosters a damaging culture of dependency among African governments.

Announcements by Marco Rubio, the secretary of state and acting head of U.S.A.I.D., that emergency food and lifesaving aid would be exempted from the administration’s cuts were initially welcomed by employees. But, officials said, it turned out to be largely a mirage. Despite the promise of waivers, many have found it impossible to obtain one.

Worst of all, many said, were the broadsides delivered by Mr. Musk and the White House portraying the agency as a rogue, criminal agency run by spendthrift officials pursuing their personal agendas. Such attacks were false and deeply hurtful to Americans who sought to relieve human suffering around the world, several people said.

In Nairobi, where U.S.A.I.D. has about 250 Kenyan and 50 American staff members, several Kenyans spoke at a tense town hall this week.

They worried that talk at the White House of widespread corruption inside the agency might cause other Kenyans to believe that they, too, had benefited from fraud, said an official who attended the meeting.

Like the Americans present at the town hall, the Kenyans worried they were about to be fired. But there was one major difference between the two groups, the official noted: While the Kenyans were anxious for their livelihoods, the Americans were worried about their country.