Thousands of demonstrators marched through the capital La Paz in support of Morales who has been granted asylum in Mexico after he was forced to step down under pressure from the military and political opponents on Tuesday.
They were demanding reinstatement of their left-wing leader, who was declared president for a fourth term in the election back in October, PressTV reported.
The opposition, however, rejected the outcome and claimed that there had been fraud in the election process.
That sparked violent street protests, which left three people dead and hundreds more wounded, in what the Morales government already called a coup bid.
On Wednesday, self proclaimed interim president Jeanine Anez appointed a new cabinet.
This brought crowds of demonstrators into the seat of government, La Paz, from the neighboring town of El Alto for the second day on Thursday, who were insisting that Morales' departure was not a resignation but rather the product of a coup.
Protesters were waving multicolored "wiphala" indigenous flags, with many of them chanting "The time is now, civil war" and "Come back Evo!"
Angry demonstrators tore off corrugated sheets of metal and wooden planks from construction sites to use as weapons, and some set off sticks of dynamite.
This has raised concerns that the country is now on the brink of a civil war.