The embattled Gutierrez left the Carondelet presidential palace just as the legislature named Vice President Alfredo Palacio as the new head of state.
He traveled by helicopter to Quito's airport, where demonstrators prevented him from leaving the country, reportedly to Panama, where his wife and two daughters are.
The helicopter then took Gutierrez to a nearby military base, where he was reportedly detained. Acting Prosecutor Cecilia de Armas said she ordered his arrest for ilegally ordering police and soldiers to crush protesters demanding his removal from office.
However late Wednesday the Brazilian Foreign Ministry issued a statement saying that Gutierrez had entered Brazil's embassy in Quito and asked for political asylum.
All three branches of the armed forces issued a communique endorsing Gutierrez's ouster.
"Ecuador's Armed Forces, respecting the presidential succession, calls for calm and peace in the country," the statement read.
Ecuadorans "cannot find a way out of the crisis if we . . . do not all collaborate to lower the tension and restore calm," the statement added.
Gutierrez, who took office in 2003, is a retired colonel best known for being one of the leaders of a coup that ousted elected president Jamil Mahuad in 2000.
He becomes the third president to be ousted since 1997, when Congress removed then-president Abdala Bucaram on grounds of mental incapacity.
"Today the arrogance and fear have ended," said Palacio, a left-wing, 65-year-old cardiologist who had been elected alongside Gutierrez.
Gutierrez earlier rejected a congressional vote to oust him from office, but reconsidered when the military made it clear they would no longer support him.
Gutierrez's authority had already been undermined by street protests that killed at least two people and wounded 100.
Sixty of the 62 lawmakers present at the session voted to oust Gutierrez, said Christian Democrat Deputy Ramiro Rivera.
Under Ecuador's constitution, the president can be dismissed for dereliction of duty.
Police and soldiers were later seen dismantling barricades and leaving the area around the presidential palace.
Gutierrez had said he would not resign, insisting that the protests were financed by business tycoons.
Worried by the mounting turmoil, the US ambassador to Ecuador, Kristie Kenney, met with Gutierrez at the presidential palace before the president fled.
In Washington, a US official questioned the legality of Ecuador's transfer of power.
"There are some constitutional questions," the official said, speaking on condition of anonymity, adding: "We are following developments very closely."
The political turmoil began in December after Gutierrez asked the legislature to dismiss 27 of 31 Supreme Court justices, a move seen by opponents as an attempt to consolidate power.
Discontent spread rapidly over the new supreme court's decisions not to put on trial former presidents Bucaram, who governed Ecuador from 1996 to 1997, and Gustavo Noboa, president from 2000 to 2003.
In April, the court allowed the two leaders, both Gutierrez allies, to return to Ecuador from their exile in Panama and the Dominican Republic.
There was also widespread discontent over the performance of Gutierrez, who rode to power with the support of indigenous groups. Rather than the economic and social reforms he promised, Gutierrez has applied austerity policies supported by the International Monetary Fund.
The Venezuelan government said it would be willing to offer asylum to Gutierrez, but declined to comment on the crisis.
In neighboring Peru, President Alejandro Toledo urged Ecuadorans to remain calm, "as Ecuador, just like Peru and Latin America need to continue to grow."
burs/ch/ceh