According to São Paulo state authorities, nine other people were injured in the rains and five more were missing, while some 500 families were left homeless across the state.
Sao Paulo Governor João Doria flew over the flooded areas on Sunday and said he had authorized 15 million reais (2.79 million USD) of emergency aid for the affected cities.
The hardest-hit municipalities around greater São Paulo included Aruja, Francisco Morato, Embu das Artes and Franco da Rocha.
The storms also caused damages upstate in Varzea Paulista, Campo Limpo Paulista, Jau, Capivari, Montemor and Rafard, state officials said.
Since December, heavy rains have triggered deadly floods in northeast Brazil, threatened to delay harvests in the midwest and briefly forced the suspension of mining operations in the state of Minas Gerais.