A group of vandals, some wearing black hoods, smashed store windows and bank ATM machines, set a public bus on fire, and destroyed subway and bus ticket machines yesterday.
Riot police wielding clubs and shields in turn fired tear gas to disperse the mob. Sao Paulo police blamed the anarchist group "Black Bloc" for the violence.
At least 78 people were arrested in the protest, police told AFP.
The protest briefly blocked key city streets and disrupted the public transportation system in the city of 11 million.
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"Since the start of the demonstration the presence of Black Bloc members, who screamed at police and tried to get them to react violently, was noticed," city police told AFP in a statement.
The anarchists "attacked Colonel Reynaldo Simoes Rossi in a cowardly fashion, stealing his pistol and his radio. The officer had his collar bone broken and multiple lacerations to his face and head," the report read.
Broadcast images showed a sole plainclothes officer waving his pistol in an attempt to guard the colonel, who was on the ground being attacked by the masked thugs.
More than a million Brazilians took to the streets in June, angry at widespread corruption and the millions being spent on the sporting events. Protesters say the money should instead be invested in improved transportation, education and health services.
In a June protest in Sao Paulo, tens of thousands marched over the poor condition of the public transportation system.
Smaller protests have since been taking place in Sao Paulo and Rio de Janeiro. Those protests are often led by radical groups and usually end up in clashes with police.