Both results were much higher than the 53.7 per cent margin he won to become president nearly three years ago, giving what appeared to be a stronger mandate to Morales's nationalist revolution.
Morales called for the vote on Sunday hoping to boost his authority over eight opposition governors who rejected his proposed measures to redistribute wealth to the country's indigenous minority.
Congress, relying on the constitution, said the president or the governors can be ousted if the number of "no" votes exceed the amount of support they received in 2005 elections.
But the National Electoral Court offered a different formula, setting Morales's bar at 53.7 per cent as per his previous mandate, but requiring 50 per cent plus one ballot to bring down a governor.
The uncertainty sparked some isolated incidents of violence ahead of the polls, but the voting itself reportedly went smoothly.
More than 100 international observers were on hand to monitor the referendum.
On Tuesday, Cristina Kirchner, Argentina's president, and Hugo Chavez, Venezuela's president, both allies of Morales, had to cancel a visit to meet him in southern Bolivia when anti-government protesters stormed the airport.
Morales's political opponents have branded the referendum "illegal" and vowed to not recognise the results.