It said the local population's high immunity to the disease "appears to have prevented transmission".
Brazil has been polio-free since 1989 and has high vaccination coverage.
The virus was found in "sewage only" and subsequent analysis of similar samples have either been negative or only positive for "non-polio enteroviruses", the organisation said.
The WHO said the sample was a close match with a recent strain isolated in a case in Equatorial Guinea.
The risk of the polio virus spreading from Equatorial Guinea is described as "high" by the UN agency, but it said the risk from Brazil remained "very low".
Polio invades the nervous system and can cause irreversible paralysis within hours. There is no cure for the disease but it can be prevented by immunisation.
Brazil's last national immunisation campaign was conducted a year ago and coverage in Sao Paulo state has been higher than 95%, the WHO said.
Polio: the facts
• A highly infectious viral disease that mainly affects children under five
• Can cause irreversible paralysis
• There is no cure, but polio vaccine given multiple times can protect a child for life
• Afghanistan, Nigeria and Pakistan are the only countries left with endemic polio