Mr Morales, the country's leader for almost 14 years, said in televised comments that he would submit his resignation letter in order to help restore stability, though he aimed barbs at what he called a "civic coup".
When it resumed, it showed a shift in favor of Morales. Morales warned that Bolivia's democracy is at risk because of the coup d'etat attempt launched by violent groups that threaten the constitutional order, and denounced to the worldwide community 'this attack on the rule of law'.
Morales earlier convened an emergency meeting with some of his ministers.
"(Mr Morales') legacy will be compromised and the region will suffer another impact with consequences well beyond Bolivia".
Morales was declared the victor by a lead of more than 10 points over the runner-up.
At a news conference later at the base, the president appealed to Bolivia's political factions to hold talks.
The Organization of American States (OAS) released a report that detailed a series of alleged irregularities in Bolivia's election, including failures in the chain of custody for ballots, adjustment and forgery of electoral material, redirection of data to unauthorized servers and data manipulation which all impacted the official vote count.
Morales took to Twitter to denounce the police rebellion as a coup. And immediately preceding the Bolivian coup, wrongfully imprisoned ex-President Lula was freed.
Earlier, Ebrard criticized the involvement of the Bolivian military in the day's events crisis, saying that "we reject it".
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The Organization of American States (OAS) is conducting an audit of the votes, and the results are expected to be published next week.
President Evo Morales was not in the compound when police retreated to their barracks, in a sign of growing discontent among security forces after a disputed election.
Morales stepped down hours after the Organization of American States released report outlining irregularities in the October 20 election. "Only when we can be sure that democracy is solid, then will we go back home".
Winning in the first round was critical for Morales, as analysts had said that he'd likely lose a runoff facing an opposition united behind Mesa.
Pressure continued to build on Mr Morales during the day, as several of his political allies resigned, some citing fears for the safety of their families.
The state news agency ABI said Morales announced his resignation from Chapare province, where he began his career as a union leader.
Bolivia's military chief says that President Evo Morales should resign so that stability can be restored after weeks of protests over his disputed election. The attorney general's office said it would investigate the tribunal's judges for possible fraud, and police later said Choque had been detained along with 37 other officials on suspicion of electoral crimes.
"I have nothing to negotiate", said opposition candidate Carlos Mesa, the runner-up in the elections.
Morales, 60, became the first president from Bolivia's indigenous population in 2006 and presided over a commodities-fed economic boom in South America's poorest country.