Apparently no one knows who will rule the country until the new elections take place or when those elections will be held (there are rumors that it would take until the second hald of next year)
The Vice President and the President of the Senate (and Provisional President) also resigned
It's not known whether the Armed Forces will take the handle of the government or if the president of the Supreme Court will assume as president, as established by the Acephaly Law. The vice-president of the Senate (from the Democrats opposition party) claims that she should be the next provisional president
The top prosecutor has ordered the arrest of all members of the Electoral Court
I highly doubt the head of the Armed Forces would formally take the mantle of power, as blatant coups have fallen out of fashion. What is more likely is that someone completely impotent (like the President of the Supreme Court) formally takes power whilst the army runs things behind the scenes.
History will doubtlessly judge Morales favorably for not clinging to power at the expense of his country's wellbeing.