Violence and political uncertainty in Yemen only grew on Thursday after President Ali Abdullah Saleh pledged to end his 33-year rule, as tens of thousands of protesters denounced the promise of immunity from prosecution given the leader and his circle, and opposition activists questioned whether he truly intended to yield control.

Associated PressDemonstrators in the Yemen capital, San’a, on Thursday denounced President Saleh, right, who signed an agreement in Riyadh on Wednesday that sets a timetable for his departure.

Armed men in civilian clothes fired into crowds of democracy activists marching in the capital, San’a, killing five young male protesters as government forces looked on, witnesses said. They drove off in military trucks.

“Let the world watch unarmed youth be killed while they insist on giving Ali Saleh immunity,” one protester, Faizah Gubari, said as the demonstration dissolved into a frenzied rush to take the dead, dying and two dozen others wounded by bullets to a clinic set up by activists. “Where is justice?” Ms. Gubari demanded. “Why is he killing and being forgiven?”

Under the agreement, a copy of which was reviewed by The Wall Street Journal, Mr. Saleh will transfer his powers to Vice President Abed Rabbo Mansour Hadi within 90 days. But the agreement is vague, and White House officials said the power transfer already took place.

Within 90 days, the deal calls for an election to be held in which Mr. Hadi, diplomats said, is expected to be the consensus candidate elected to a two-year term in which he would prepare the terrain for parliamentary elections, a new constitution, fresh electoral laws and reforms to the military.

U.S. officials on Thursday said they were hopeful of a successful transition because Mr. Saleh signed the deal Wednesday—in an unannounced trip to Saudi Arabia—in the presence of Saudi and United Arab Emirate leaders whose support he needs.

If the deal holds, Mr. Saleh would be the fourth leader to lose power in the wave of this year’s Arab Spring uprisings, after autocrats in Tunisia, Egypt and Libya.

Still, several previous breakthroughs with Mr. Saleh fell apart at the last minute, and U.S. officials acknowledged the potential for this one to sink before new presidential elections.

Mr. Saleh’s signing of the pledge was only “the beginning of an agreement to initiate the transition of power,” rather than an actual ceding of power, said Ginny Hill, a Yemen analyst with Chatham House in London. “The question is when and how the transition deal gets delayed or derailed, and who is held responsible.” Ms. Hill added that “everyone in Yemen’s political system is now rapidly recalculating the balance of power and reconsidering their options.”

Senior Yemen security officials and a Western diplomat said that after Mr. Saleh resisted for months, he relented to stepping down only after U.S. and European Union authorities threatened him and senior figures in his government with an asset freeze and a travel ban. “Saleh was under serious warnings and he knew he had nowhere to run,” one official said.

U.S. State Department spokeswoman Beth Gosselin declined to comment on whether Mr. Saleh stepped down for that reason.

Mr. Saleh’s immunity is contentious. The deal calls for him and his aides to retain immunity while he remains in office, giving the Yemeni Parliament time to pass a law that could protect them from prosecution.

But with street tensions boiling over, it is unclear how such a law would fare in Parliament, officials and observers said.

Another scenario that could hamper any transition is that Mr. Saleh’s son and nephews still run the country’s best-trained and best-equipped security units. European officials have told Mr. Saleh they will renew a push for sanctions if his family doesn’t relinquish its control of the forces within three months.

Still, several government officials indicated on Thursday that Mr. Saleh’s family may retain control of those security forces.

“The president’s sons and nephews will continue serving the country,” one senior presidential official said on condition of anonymity, saying he wasn’t authorized to speak to reporters.

The country’s counterterror branches—built up by the U.S. and Britain so that Mr. Saleh’s government could better fight a Yemen-based branch of al Qaeda—allegedly have attacked unarmed protesters and in battles with tribal factions and breakaway army units that sought Mr. Saleh’s departure.

In anticipation of Mr. Saleh’s eventual departure, the Pentagon has taken steps to try to ensure that counterterrorism cooperation against al Qaeda in the Arabian Peninsula will continue regardless of who is in power, U.S. officials said. These steps have included building relationships with a wide range of military commanders and counterterrorism leaders who could remain in positions of influence post-Saleh.

With no official release of the deal Mr. Saleh signed and no public word from Vice President Hadi, activists were suspicious over the deal’s terms. That uncertainty raised the specter of more chaos and fighting aheadin Yemen, the Arab Peninsula’s poorest country.

Supporters of the accord hope the transition agreement will end 10 months of violence against democracy activists demanding Mr. Saleh’s departure.

Yemen’s most prominent rights organization, HOOD, said that more than 1,000 unarmed civilians have been killed by pro-government forces since calls for regime change began in January.

“The death toll continues to increase and that is why it will be almost impossible for millions of youth protesters to accept immunity for Saleh,” said Mohammed Allow, HOOD’s president.

Tribal fighters and breakaway army factions have battled loyalist forces in the streets of the capital. Security units led by Mr. Saleh’s male relatives are persisting in shelling opposition neighborhoods in a second, southern city, Taiz.

Mr. Saleh withstood months of international pressure attempting to prod him from power, as well as an apparent assassination attempt at the presidential palace in June that left him badly wounded by a bomb.

U.N. Secretary-General Ban Ki-moon said Wednesday after a phone call with Mr. Saleh, believed to still be suffering from internal injuries after the bombing, that the president would soon fly to New York City for medical treatment.

The U.S. has been informed that Mr. Saleh expressed his desire to get medical treatment in New York, but that he wasn’t seeking asylum, a U.S. official said.

On Thursday, activists in San’a pledged to continue their demonstrations pressing for democracy in Yemen. “Our revolution will continue, so beware, Saleh,” they chanted.

Leaders of the most powerful opposition factions in Yemen—Ali Mohsen al Ahmar, the general who commanded breakaway military units, and leaders of the al-Ahmar family, leaders of the country’s most powerful tribe—have made no public comment since Mr. Saleh’s signing of the resignation deal.

In San’a on Thursday, one of the youth leaders of the uprising said democracy activists would stay in their tents in San’a’s Change Square until elected civilian leaders oversaw Yemen’s security forces.

“We are seeking justice and a nation for all,” the protester, Khaled Anesi, said. “From today, no more families in control of the military.”

—Adam Entous, Alicia Mundy and Jay Solomon contributed to this article