Vice President Alvaro Garcia Linera also resigned after Morales stepped down on Sunday, reports Efe news.
The two men appeared together in a video in which they issued a call for calm and peace in Bolivia.
In the video, Morales lamented what he said was a "civic coup" against him and called on opposition leaders Carlos Mesa and Luis Fernando Camacho, whom he accused of staging the "coup" to oust him, not to "mistreat" Boliv and "stop kicking" them.
"We don't want confrontations," he said, adding that he was resigning to foster the "pacification" of Bolivia and so that the country could "return to social peace".
The country has been going through a serious crisis since the October 20 election, in which Morales was proclaimed the outright winner but the opposition claimed that fraud was committed to keep him in power and called for him to resign.
"The struggle doesn't end here," Morales warned, saying that a "civic, political and police coup" had been instigated against him by "oligarchic groups that are conspiring against democracy".
He also said that he was saddened by the violence in recent days, adding that he will be in the Cochabamba area, the portion of Bolivia in which he began his political career, after a series of rumours that he had - or would - leave the country.
"I have no reason to leave," Morales declared, "because I haven't stolen anything".
Opposition candidate and former President Carlos Mesa, meanwhile, hailed the development, calling it as "the end of the tyranny".
"To Bolivia, to her people, to the young people, to the women, to the heroism of the peaceful resistance. I will never forget this unique day. The end of the tyranny. Grateful as a Bolivia for this historic lesson. Long live Bolivia," Mesa tweeted.
Earlier on Sunday, the armed forces and National Police had called on Morales to resign as a step toward restoring calm in Bolivia, which has been rocked by protests.
Also on Sunday, Morales said a new presidential election would take place in Bolivia and the results of the vote held last month would be annulled.
Morales's announcement came after the Organization of American States (OAS) released a report recommending that a new presidential election be held due to the irregularities in the October 20 vote.
Pro- and anti-government protesters have been clashing since the day after the election, leaving at least three people dead and 421 others injured, according to official figures.
On Sunday, at least three people were wounded when someone opened fire on a highway in the highlands on a caravan of buses carrying miners headed to La Paz to join the protests against Morales.
( With inputs from IANS )