Demonstrators supporting Morales and backers of opposition leader Carlos Mesa also clashed in downtown La Paz, while police fired tear gas to disperse both sides.
Violent clashes a day earlier left 40 people injured in the cities of Cochabamba and Santa Cruz. Police said 20 people were detained.
Santa Cruz, an eastern city that is a stronghold of opposition sentiment, has been paralyzed by protests.
Speaking to a large crowd of supporters in the city of El Alto on Monday, Morales proclaimed victory.
"Show us where there was fraud," said Morales, who denies irregularities and says he welcomes an international audit of the election. The leftist leader accused "the right" of trying to orchestrate a coup d'état.
Conservatives have always distrusted the leader of the Movement Toward Socialism party who has been in power for nearly 14 years. Many were also angered by his decision earlier to seek another re-election despite a popular referendum that upheld term limits. A Supreme Court ruling made it possible for Morales to run, in the end.
"The critical factor is whether the historic citizen mobilizations in Bolivia today can be sustained over time, which would render the country virtually ungovernable," said Michael Shifter, president of the Inter-American Dialogue and professor of Latin American politics at Georgetown University.
"The country's social and economic progress under three Morales administrations is undeniable, but does not mean, as he seems to believe, that the positive record entitles him to another term, no matter what the constitution says or what the citizens decide."