Critics interpreted the troop deployment as a sign of desperation by a president fighting for his political life after a corruption scandal reached his doorstep.
A decree published online in the official journal yesterday said the president had revoked a measure to deploy 1,500 federal troops -- a delicate issue in a country with living memory of a military dictatorship.
Soldiers shortly afterwards began to withdraw from around government buildings which they had spent the night guarding in Brasilia.
Protesters smashed their way into ministries and fought with riot police on Wednesday in some of the most violent scenes yet in a year of political turbulence.
Defense Minister Raul Jungmann insisted yesterday the deployment was necessary "to stop the barbarity" of the riots.
"We had no choice in order to prevent casualties among public servants and the destruction of public heritage," Jungmann said.
But the issue of troops is sensitive in a country that lived under military rule from 1964-1985.
Columnist Maria Cristina Fernandes in economic daily Valor described the deployment as "the last chance for a show of authority by a government that is finished."
She was impeached for illegally manipulating government accounts, but said the charges were politically trumped up.
Now Temer faces impeachment requests from his own political rivals.
Violence erupted on Wednesday after a crowd of demonstrators, estimated by police at 45,000, marched toward the presidential palace, which is flanked by Congress and the government buildings.
Most of the protesters were peaceful but small groups wearing masks threw stones at police and smashed their way into the agriculture ministry and reportedly also the culture and planning ministries.
Riot police crouching behind black shields lobbed tear gas and stun grenades into the crowd.
In the lower house of Congress, the session was temporarily suspended after leftist deputies took over the speaker's podium, brandishing signs saying "Temer out."
According to a count released by authorities, 49 people were injured and seven detained in the protests.
Leftist groups and trade unions organized the protests a week after Temer was placed under a corruption probe.
They are demanding his resignation and an end to austerity reforms centered on cuts to the pension system.
Stuck in deep recession for two years, Latin America's biggest economy is just showing signs of returning to growth, although unemployment stands at nearly 14 percent.
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