Strikes and protests were held on Wednesday, which were called by the Central Obrera Boliviana (COB), a powerful labour federation, in support of indigenous activists who have been marching towards La Paz to protest a planned road in the Amazon.
Thousands marched from the suburb of El Alto into the capital, chanting "Evo is a fascist!" and "Evo is a lackey of Brazilian companies" expected to build the road, as miners set off sticks of dynamite.
Authorities had initially called the strike unnecessary as Morales had already late Monday suspended plans to build the road, and the controversy has seen two government ministers resign.
But late Wednesday Morales, the country's first elected indigenous president, apologized for Sunday's violence -- in which police fired tear gas at marchers -- and called for new talks with local residents.
"Forgive me. Pardon me. There was no order (to disperse the protest), Morales said. "There was no presidential order."
"We should convene a new dialogue, and we are here to continue the dialogue," he said, calling the protests a "wake-up call from the Bolivian people."
Bolivian authorities have been attempting to tamp down on the uproar that erupted after riot police fired tear gas and arrested hundreds of activists who had been marching for a month.
Bolivia's interior minister Sacha Llorenti resigned from Morales's leftist government on Tuesday over the violence, a day after defence minister Cecilia Chacona also left office in disgust over the incident.
Migration chief Maria Rene Quiroga has also resigned over the crackdown, calling it "unforgivable."
The protests and popular fallout from the crackdown present a major challenge for Morales, who has said the 300-kilometer (186-mile) highway is vital for economic development in South America's poorest country.
The Brazil-financed road would run through a nature preserve home to some 50,000 natives from three different indigenous groups.
The road is part of a network linking land-locked Bolivia, South America's only mostly indigenous nation, to both the Pacific through Chile and the Atlantic through Brazil, a key outlet for Bolivian exports.
The government says it would be too costly to build the highway around the preserve.
Amazon natives also fear landless Andean Quechua and Aymara people -- Bolivia's main indigenous groups and Morales supporters -- will flood into the road area and colonize the region.