Heavily armed police spirited Lucio Gutierrez to an air base south of Quito from the Brazilian embassy residence, where the retired military officer had taken refuge after he left the presidential palace last week.
From there Mr Gutierrez flew to political asylum in Brazil, accompanied by his family.
In a letter requesting asylum given to reporters, the deposed leader wrote:
“In light of the current situation in the Republic of Ecuador, I feel personally threatened and unable to guarantee my liberty and physical integrity, as well as of my wife’s and of my daughters.”
Enemies of Mr Gutierrez accuse him of corruption, abuse of power and the violent repression of protests that prompted Wednesday’s congressional vote to oust him.
The former president dissolved the Supreme Court a week ago in hopes of placating demonstrations who accused him of stacking the court in his favour, but the move backfired and set off even more massive protests.
The streets of the capital appeared calm with no signs of reaction to the departure of Mr Gutierrez.
The former president is the third leader of the oil-rich Andean country forced from office in eight years.
In Ecuador, supporters of Mr Gutierrez argued he was ousted illegally and will return to his homeland.
Congress fired Mr Gutierrez from the presidency on Wednesday for abandoning his post and replaced him with Alfredo Palacio, his vice president.
The Organisation of American States has called on Ecuador’s new government to explain how Congress justified its decision to remove him for “abandonment of the post” when he was still in the Government Palace issuing orders.