Two people were fatally shot at around midnight Wednesday during clashes between supporters and opponents of Morales in Santa Cruz province, an opposition stronghold.
On Friday, the government confirmed that a delegation from the Organisation of American States had arrived and started an audit of the election results. The audit is expected to take 10 to 12 days.
The opposition, led by former president Carlos Mesa, rejects the audit. He says its terms were agreed upon "unilaterally" by the government and the OAS, without consulting the opposition or other civil society groups.
Mesa came less than one percentage point away from forcing a runoff against Morales, who has been in power for 14 years. Suspicions about electoral fraud arose following a 24-hour halt in the reporting of vote results.
With Morales at the helm, Bolivia has seen commodities-fueled economic growth. But voters have been angered by his refusal to accept the results of a 2016 referendum to keep limits on presidential terms. A subsequent decision by the country's top electoral court allowed him to seek a fourth term.