But though he may win the vote, the result is unlikely to end the stand-off with his rivals, with analysts warning that conflicting rules on how to interpret the results could create confusion.
According to congress, which is relying on the constitution, Morales or the governors can be ousted if the number of 'No' votes exceed the amount of support they received in 2005 elections.
Thus Morales could be forced out if more than 53.74 per cent of voters go against him, while the governors can be toppled with just 38 to 48 per cent of ballots.
But the National Electoral Court has offered a very different formula: Morales's bar remains at 53.74 percent, but the proportion needed to bring down a governor is 50 per cent plus one ballot.
The uncertainty sparked some isolated incidents of violence ahead of the polls.
On Tuesday, Cristina Kirchner, Argentine president, and Hugo Chavez, Venezuelan president, both allies, had to cancel a visit to see Morales in southern Bolivia when anti-government protesters stormed the airport.
Morales' political opponents have branded the referendum "illegal" and vowed to not recognise the results.