The STF's decision acknowledges that President Jair Bolsonaro has been unable to take the necessary measures to contain COVID-19 in the country, which has been hit hardest by the pandemic in Latin America.
"The STF's verdict is a defeat for the Brazilian president," teleSUR's correspondent in Brazil, Andre Vieira, said on his Twitter account.
The Supreme Court also rejected a request by Bolsonaro that sought to focus the country's decisions on the pandemic.
The state and municipal governments will autonomously take measures to define isolation, quarantine and restriction of transportation and transit on the roads.
El Supremo Tribunal Federal de #Brasil decidió hoy que los gobiernos locales pueden imponer medidas restrictivas para contener el COVID-19 y rechazó una solicitud de Jair Bolsonaro que pretendia concentrar las decisiones.
"Defeat for Bolsonaro. Brazil's Federal Supreme Court decided today that local governments can impose restrictive measures to contain COVID-19 and rejected a request by Jair Bolsonaro to concentrate the decisions."
The decision was taken amid a backdrop of tensions between the health sector and President Bolsonaro.
The Health Surveillance Secretary of the Ministry of Health, Wanderson de Oliveira, recently presented his resignation from the post due to differences with right-wing extremist Bolsonaro in the management of the health crisis.
The official's resignation was not accepted by Health Minister Luiz Henrique Mandetta, and he managed to convince him to remain in office.
"He said he was leaving, I said I didn't accept. And here we are. We will get out of this together" Mandetta said at a press conference held with De Oliveira.
This Wednesday, Brazil reached 28,320 confirmed cases of Covid-19, with 1,736 deaths.