They left a trail of rubble down the protest routes.
While asking police to back off from peaceful protesters, Rousseff has condemned "isolated and minor acts of violence," telling police to confront them "with vigor."
In light of the protests, the Brazilian president has postponed a trip to Japan, the state-run Agencia Brasil news agency reported Thursday.
Rousseff had been scheduled to travel to Japan on June 23-28, the government news agency reported, citing the president's communications secretary. A new date for the trip has not been announced, Agencia Brasil said.
Weeks of protests
For nearly two weeks, tens of thousands of Brazilians marched through the streets night after night.
Crowds originally protesting bus fares grew into multitudes decrying social injustice on Tuesday, as broad avenues filled to capacity for blocks.
The protests come amid the soccer Confederations Cup tournament, a friendly array of matches, in which the host country, Brazil, plays against a small group of national teams from around the globe. The cup serves as a precursor to the World Cup.
The majority of marchers are young and well-educated.
Matheus Pires, a university student and one of the organizers, says public transportation should be free -- especially in expensive, sprawling cities such as Sao Paulo.
"You can't go to hospital; you can't see your friends; you can't go to school; you can't go to work," he said, describing how much the city's residents rely on mass transit.
Lowering fares, he said, would prove that the government was listening.
But it's too soon to know whether it will bring an end to protests or fuel further and more far-reaching demands.