The diagnosis capped a health scare triggered by the death Tuesday of the 53-year-old man, who is believed to have contracted the illness in his home country.
Initially, it was feared he might have succumbed to an arenavirus, a highly contagious, often deadly group of hemorrhagic diseases endemic to parts of Africa.
One arenavirus was present in a Johannesburg hospital where the man had undergone an October operation, weeks before his arrival in Brazil on November 23. He was admitted to hospital two days later suffering vomiting, rashes and fever.
Medical staff who treated the man in Rio de Janeiro had been put under observation and South African authorities were contacted to help identify the illness.
The body of the man, identified in Brazilian media as William Charles Erasmus, was cremated as a precaution last Thursday by a special decontamination team wearing sealed suits.
Authorities at the health ministry in the state of Rio de Janeiro said tests at a lab specializing in viruses, the Oswaldo Cruz Foundation, determined the bacteria from its genome contained in blood samples.
"There is no risk of person-to-person infection. The Rickettsia bacteria is only transmitted by ticks," the deputy head of the lab, Ary Carvalho de Miranda, told reporters.
Brazil itself has registered 641 cases of spotted fever in the past decade. The disease is fatal in 30 percent of cases.