Many of the subway lines were not operational Thursday which caused citizens to resort to the railway system, buses and cars, leading to huge traffic jams, Xinhua quoted the daily O Globo as saying.
The report also said the morning traffic was the third slowest in history, and thousands of citizens were not able to get to work.
It is not the first time Sao Paulo faced transportation problems: bus drivers went on strike for two days in May and passengers were left without a lot of options.
The subway and the railway lines do not cover the entire city and are not sufficient to deal with the extra number of passengers.
Sao Paulo will host the World Cup's opening match, Brazil versus Croatia, June 12 as well as other five matches, including a semifinal. Most of the match goers are expected to get to the stadium by public transport, including the five subway lines in the city.