Officials said Morales, who came to power in 2006, won 47.1 per cent of the vote and beaten his closest rival Carlos Mesa, who has accused the incumbent of fraud, by more than 10 percentage points or 36.51 per cent, thereby avoiding a run-off, the BBC reported.
The remaining 0.01 per cent of votes were voided in the region of Beni, with new voting there scheduled for November. These votes would not be enough to change the outcome of the election, a spokeswoman for the electoral tribunal said.
Morales, Bolivia's first indigenous President and already Latin America's longest-serving leader, was now set to govern the country until 2025.
Claims of vote-rigging were made after the count was interrupted for 24 hours.
Mesa has called for a second-round vote as have the US, Brazil, Argentina and Colombia.
In a video released after counting ended, Mesa said: "We're witnessing a crucial moment in history," adding that the numbers were irrelevant because Morales had orchestrated a "shameful and rude alteration of results".
Meanwhile on Thursday, police fired tear gas at crowds who protested by the thousands in the capital, La Paz.
Clashes also broke out in Santa Cruz de la Sierra, the country's largest city and an opposition stronghold.
Many Boliv have said that they no longer have confidence in the electoral authorities, and more protests against the outcome were expected on Friday, the BBC reported.
Protests have been held across the country since Monday, with electoral offices in Sucre and Potosi being torched.
A general strike began on Wednesday, and Mesa has urged his supporters to continue protest action.
( With inputs from IANS )