Putin embraced turmoil, and now it is rattling his leadership.

President Vladimir V. Putin of Russia always seemed to thrive on chaos. Then it threatened to consume him.

For the last few months, as the mercenary chieftain Yevgeny V. Prigozhin escalated his feud with the Russian military, Mr. Putin did not publicly reveal any discomfort with his diatribes. The silence fostered the kind of political ambiguity that has long been a trademark of Mr. Putin’s rule: tolerating, even encouraging, conflict among the elite because it kept potential rivals in check, while underscoring that ultimate authority always rested with the president himself.

The Russian leader’s key litmus test was loyalty — a fact that Mr. Prigozhin showed he understood, even amid his recent criticism of the military leadership: “I listen to Putin,” he said in May. And yet on Saturday, after more than 20 years profiting from his personal ties to Mr. Putin, Mr. Prigozhin cast the last shreds of that loyalty aside and plunged Russia into its biggest political crisis in three decades, as his forces seized control of key military facilities in the southwestern city of Rostov-on-Don and threatened to enter Moscow.

The specter of a pitched battle for Moscow appeared averted — at least for the moment — on Saturday night, after Mr. Prigozhin declared that he was turning around his troops who had been marching toward the Russian capital.

But at no point since being named acting president on Dec. 31, 1999, had Mr. Putin faced such a dramatic challenge. And it came from a man who — like much of Russia’s elite — owes his power and status to the informal, personalist style of the Russian president.

“Putin underestimated” the threat posed by Mr. Prigozhin, said Tatiana Stanovaya, a senior fellow at the Carnegie Russia Eurasia Center. “He thought he was totally dependent and loyal.”

Mr. Putin’s patience with Mr. Prigozhin’s outbursts this year may have served his political purposes, but it prompted officials stunned by Mr. Prigozhin’s verbal attacks on Russia’s top brass to conclude that he enjoyed the president’s tacit support, analysts said. It also further emboldened Mr. Prigozhin, who even as he launched his armed rebellion insisted that “this is not a coup” and that “presidential authority” would remain in place.

The confusion over Mr. Putin’s personal views only came to an end Saturday morning, when the president delivered a five-minute address to the nation describing Mr. Prigozhin — without naming him — as a traitor and vowing to quell the uprising the paramilitary leader had started. But the damage had already been done.

Throughout Saturday’s drama, there were no immediate signs that Mr. Putin’s hold on power was about to crumble, with no one in the Russian elite publicly siding with Mr. Prigozhin. Other powerful men at the nodes of Mr. Putin’s informal power structure — like Ramzan Kadyrov, the strongman leader of the southern Russian region of Chechnya, who controls his own paramilitary force — voiced their support for the president on Saturday.

To be sure, amid the fast-moving developments, there was no way to know whether Mr. Prigozhin may have garnered some support behind the scenes. Nor was it clear what would come of the deal he struck with President Aleksandr G. Lukashenko of Belarus, whose government announced late Saturday that it had brokered an agreement to defuse the crisis.

The events were a striking consequence of the informal power structure that Mr. Putin built up in his 23 years at Russia’s helm. For more than two decades, the system helped Mr. Putin secure his unrivaled authority, ensuring that he personally held the keys to wealth and influence in modern Russia.

People who know Mr. Putin say that the president has always been comfortable with that personalized system, because it allowed him to entrust key tasks to a trusted inner circle while preventing the rise of rival cliques that could undermine him. And it ensured that the institutions of the state — from the courts to Parliament to the news media to the multiple security services — remained mere instruments in internecine power plays mediated by Mr. Putin, rather than sources of influence in their own right.

Shortly after taking power, Mr. Putin used brute force to crush the “oligarch” business tycoons who held immense sway over President Boris N. Yeltsin in the 1990s. He then allowed competition among rival groups to fester, even fostering security agencies with overlapping responsibilities; for instance, an Investigative Committee, a Prosecutor General and a Federal Security Service are all involved in investigating crimes.

In the war-torn Chechnya region, Mr. Kadyrov built up a private fief while professing loyalty to no official but Mr. Putin himself.

One Russian business tycoon, reflecting on Mr. Prigozhin’s rise while speaking on the condition of anonymity, said that Mr. Putin’s approach to his rule was always “divide and conquer.” As another put it, referring to Russia’s rival law enforcement authorities: “You never know who will arrest you.”

Mr. Putin’s strategy extended beyond Russia to foreign policy; he preferred to keep the world guessing about his intentions, as when his invasion of Ukraine in February 2022 stunned friend and foe alike.

But for those who did navigate that system, the rewards were stupendous. A judo sparring partner from Mr. Putin’s youth became a construction billionaire and built Mr. Putin’s landmark bridge to Crimea. Fellow K.G.B. veterans now oversee Russia’s military industrial complex and its oil sector. A friend from 1990s St. Petersburg is entrusted with control of Russia’s most important private media assets and of the bank said to be at the nexus of Mr. Putin’s own financial dealings.

And then there was Mr. Prigozhin, who has said that he met Mr. Putin in 2000 as a St. Petersburg restaurateur. He parlayed those personal ties into lucrative government contracts and styled himself as a ruthless, multipurpose problem solver for the Kremlin.

In 2016, as the Kremlin sought to swing the American presidential election to Donald J. Trump, Mr. Prigozhin jumped into the fray with an internet “troll factory,” waging “information warfare against the United States.” As Russia sought to expand its reach in Syria and Africa, Mr. Prigozhin deployed his growing Wagner mercenary force to those regions — allowing the Kremlin to project power while minimizing Russian military boots on the ground.

In Ukraine, as Mr. Prigozhin tells it, Wagner troops were only called in after Mr. Putin’s initial invasion plan failed. For much of the war’s first year, Mr. Prigozhin appeared above the law, as he toured Russian prisons to recruit thousands of convicts to bolster his force.

By early this year, the Kremlin appeared to be taking some steps to limit Mr. Prigozhin’s rise. Television commentators were directed to avoid mention of him on air, and he lost his ability to recruit convicts.

But Mr. Putin seemed to vacillate on his own support for Mr. Prigozhin. In May, he congratulated Wagner mercenaries for their role in the capture of the Ukrainian city of Bakhmut, in a statement posted on the Kremlin’s website. Weeks later, he backed the Defense Ministry’s push for mercenaries to sign service contracts with the Russian military by July 1, a demand that infuriated Mr. Prigozhin.

Many believed that the president saw good reason not to put a final stop to Mr. Prigozhin’s social media attacks on the Defense Ministry, which he characterized as inept, corrupt and indifferent to soldiers’ lives. Some analysts say Mr. Putin saw him as a useful figure — a check against the risk that a military leader could become overly popular.

Mr. Putin “needs someone quite weak and compromised” to represent the army politically, because in Russia, “even the most disastrous wars produce very popular generals,” said Andrei Soldatov, an expert on Russian intelligence and a senior fellow at the Center for European Policy Analysis. “His scheme was to keep Prigozhin talking, but he miscalculated.”

As a result, as Mr. Putin scrambled to put down a rebellion that he warned on Saturday could lead to “anarchy and fratricide,” Mr. Prigozhin loomed as the Russian president’s own creation.

Mr. Prigozhin “had no real independent power base except the favor of the president,” Mark Galeotti, an expert on the Russian military and security services, said. “However this goes, it undermines Putin’s credibility and legitimacy.”

Neil MacFarquhar and Valerie Hopkins contributed reporting.