If approved by voters, Morales' constitution would outline a detailed bill of rights and considerable autonomy for the country's 36 indigenous groups, who say they were shut out of power by the white population.
Alvaro Garcia , the vice-president, said that Morales is expected to sign the referendum into law on Friday.
Opposition politicians say the charter favours the native communities over the rest of the population and fails to address demands for autonomy from the eastern states.
They are fighting Morales' land and wealth redistribution plan and want to keep more of the region's gas revenues.
Morales has called for a May 4 referendum - the same day that the eastern state of Santa Cruz, home to his fiercest opposition, will hold a vote on a proposal to declare autonomy.
Three other opposition-controlled eastern states are expected to follow suit later in the year.
The vote took place on Thursday while hundreds of pro-Morales farmers and miners demonstrated for three days outside congress in support of the referendum.
Most opposition legislators were blocked from attending the session by a crowd of flag-waving Morales supporters and miners in hardhats who seized the plaza outside the congressional building.
Riot police largely abandoned the plaza in front of the congress on Thursday afternoon, granting control of the building's access to the pro-Morales crowd.
Immediately after the referendum passed, however, riot police reappeared to clear the congress steps.