Associated PressA Yemeni army officer reacts holding up his AK-47 as he and other officers join anti-government protestors demanding the resignation of Yemeni President Ali Abdullah Saleh, in Sanaa,Yemen, Monday.

A contingent of Yemen’s key military commanders defected to the political opposition Monday, the most significant challenge yet to the ability of the country’s president, a U.S. ally against al Qaeda, to hold on to power.

The development followed a bloody weekend crackdown on pro-democracy protesters that left dozens dead, as other countries in the region tipped toward instability. In Syria, residents of a town south of the capital demonstrated against the government for a fourth straight day, undeterred by protester deaths and the authoritarian regime’s threats of crackdown.

In Yemen, the defections put President Ali Abdullah Saleh in the position of choosing between sending his elite units into battle to defend his authority or negotiating his own exit, officials from the government and the opposition said.

The president has the loyalty of the country’s best-equipped forces, including the U.S.-trained Republican Guard, which is led by his son Ahmad, a counterterrorism liaison with Washington.

As night fell in the capital, San’a, tanks from the Republican Guard were deployed around the presidential palace; nearby stood tanks from the army division commanded by Maj. Gen. Ali Mohsen al-Ahmar, a top general who withdrew his support for Mr. Saleh earlier in the day.

Republican Guard tanks loyal to the president also stood sentinel at the central bank and state television building, according to residents.

For the U.S., the prospect of an emerging civil war in Yemen and the possibility of losing a controversial but key ally in the war on terror has emerged as a significant national-security concern. Yemen’s al Qaeda affiliate has used bases in tribal areas outside of Mr. Saleh’s control to launch failed bombing attempts on U.S.-bound planes.

Washington has encouraged Mr. Saleh to loosen the reins and adopt democratic reforms, while spending tens of millions of dollars training his forces to aid in counterterrorism operations.

Monday’s standoff opened the unsavory possibility that U.S.-trained forces could be unleashed to defend the embattled leader. The White House issued a statement saying violence in Yemen would be “unacceptable.”

The Yemeni president dispatched his foreign minister to neighboring Saudi Arabia to discuss the situation with the Saudi king, considered Mr. Saleh’s strongest foreign benefactor. Mr. Saleh said “the majority” of the country backed him, the state news agency reported.

Mr. Saleh and Gen. Ahmar, the rebel general, exchanged messages through a mediator in efforts to broker an end to the tension, according to a Yemeni official. The official also confirmed that Saudi Arabia was involved in brokering a peaceful transition of power.

Saudi Arabia has helped prop up President Saleh for much of his three decades in power, primarily as a bulwark against extremist threats aimed at the Saudi royal family.

The Saudis also have been financial patrons for many Yemeni tribal figures, giving them leverage to influence how the situation plays out in San’a, according to people familiar with the situation.

The big U.S. concern about the possible ouster of Mr. Saleh is the disposition of the leader who succeeds him; such concerns have been cited by U.S. and Arab officials in explaining their support for the Yemeni president in recent years.

One scenario, if Mr. Saleh were to be removed from power, is a broken state in which terrorism flourishes; another, a tribal-based government unfriendly to the U.S.

A third outcome would be a military-backed leadership that is friendly to the U.S. and Saudi Arabia. Yemeni opposition activists said they were wary of a wide-ranging Saudi role in Yemen, given the conservative kingdom’s own reticence to enact political reform.

Saudi Arabia also stepped in recently, against U.S. wishes, to help the Sunni royal family in Bahrain, sending troops to support the monarchy against majority Shiite protesters. That deployment was followed by an intensified Bahraini crackdown on opposition activists.

Some members of the military in Yemen throw in their support for anti-government protesters dealing a blow to President Saleh as he clings to power. Video and image courtesy of Reuters.

In Yemen, forces aligned against President Saleh coalesced rapidly over the weekend in the wake of a bloody crackdown against demonstrators who had been camped out in San’a for weeks demanding political overhauls and the resignation of the leader.

Plainclothes gunmen set up on rooftops overlooking the plaza filled with protesters shot and killed more than 50 people and wounded dozens more, according to doctors and witnesses.

The attack catalyzed an anemic protest movement led by opposition parties with unproven grass-roots support and youth activists whose reach didn’t venture far from the capital.

By the weekend, leaders of the nation’s largest tribes, including Mr. Saleh’s own, came out against the president.

On Sunday, Mr. Saleh sacked his government in a bid to assuage criticism of his rule, and state television announced that an investigation into Friday’s shooting. The government said it had arrested 16 suspected gunmen.

On Monday, many of the country’s elite who hadn’t yet taken sides in the dispute declared their loyalties in favor of the protest movement.

Gen. Ahmar, the rebel military commander, served with President Saleh for more than 30 years and was considered one of his closest confidantes.

He was joined by at least four other generals, while local media reported the defections of at least one dozen other officers from the standing army as well as at least one governor and one mayor.

“The crisis is getting more complicated and it’s pushing the country toward violence and civil war,” Gen. Ahmar—who commands an armored infantry division—said in a statement broadcast by al-Jazeera.

Yemen’s defense minister, Nasser Ahmed, spoke on state television Monday evening saying the army still supported the president and would defend him against any “coup against democracy.”

It is unclear if Gen. Ahmar’s military division has received any U.S. military assistance; much of U.S. aid has been channeled to units under the command of Mr. Saleh’s son and nephews.

Mr. Saleh, 66 years old, has been an on-and-off ally of the U.S. in the campaign against al Qaeda. U.S. officials have said the political unheaval has made it difficult for the U.S. to resume airstrikes in Yemen, which were halted in May. Pentagon officials said they were closely following events, which U.S. officials described as “fluid.”

“No one in their right mind would predict what might happen in a place like Yemen, but it’s true that Saleh’s political support has eroded in recent weeks, including inside the Yemeni government,” a U.S. official said.

A senior U.S. military official said the chance of Mr. Saleh surviving was less than 50%.

—Erik Stier, Adam Entous and Matthew Rosenberg contributed to this article.

Write to Margaret Coker at margaret.coker@wsj.com