A header from central defender Rhodolfo and Ademilson's second-half strike completed the win for Sao Paulo, who maintained their two-point lead at the top of the competition.
Sao Paulo went ahead in the fourth minute when a low free-kick from the left, clipped the Penepolense wall and ballooned to Fabricio, who flicked the ball on with his head to Rhodolfo.
The 26-year-old central defender controlled the ball with his right foot and stabbed it home with his left to put Sao Paulo 1-0 ahead.
The 21-time state champions doubled their lead in the 70th minute when Ademilson brought Maicon's long pass down and then unleashed a long-range strike past Penepolense goalkeeper Roni.
Sao Paulo have 22 points from their nine games, two ahead of Mogi Mirim and Ponte Preta, who have both played 10 matches.
Mogi Mirim also won on Sunday, knocking off Guarani 2-0 thanks to second-half goals from Roger Gaucho and Wagner.
Guarani had Leandro Souza sent off in the 80th minute for his second yellow card.
In other results, Sao Bernardo defeated Ituano 2-0 and Santos were held to a scoreless draw at home by Corinthians.