"La Paz has experienced a night of terror," the capital's mayor Luis Revilla said, adding that 64 buses were destroyed in the disturbances.
Thousands of commuters were forced to walk to work in the morning drizzle as the city's cable-car network remained paralyzed and buses scarce.
The police - largely confined to barracks since riots broke out on Friday, with many units joining the protests - were returning to the streets, police chief Vladimir Yuri Calderon said. "The Bolivian police will be acting," Calderon told ATB television.
However, the UN Secretary General Antonio Guterres voiced disquiet over the security situation in the country that seemed increasingly rudderless, and the Organization of American States (OAS) called for "peace and respect for the rule of law".
The Washington-based institution called in a statement for "an urgent meeting" of Bolivia's Congress "to name new electoral authorities to guarantee a new electoral process." The call came after Security Minister Carlos Romero, who has responsibility for the police, took refuge at the Argentine embassy, a foreign ministry source told AFP in Buenos Aires.
Several of Morales' ministers and top officials resigned after his announcement - including many who sought refuge at the Mexican embassy - raising the question of who was in charge, given that vice president Alvaro Garcia Linera also resigned.
Under the constitution, power then passes to the president of the Senate and the speaker of the lower house of Congress, in that order. But they have resigned, too.
An opposition senator, Jeanine Anez, said she would assume the interim presidency, given her position as deputy senate leader. But Congress will first have to be convened for a vote to take place and that was proving impossible on Monday as most lawmakers were in their constituencies and unable to return to La Paz.
Tweeting from the central coca-growing region of Chapare, where he fled on Sunday, Morales called on the opposition to "assume its responsibility" after Sunday's riots.