The home side dominated from start to finish with Lucas Moura reintroduced to the first eleven, going 1-0 up after Paulo Miranda tapped in a loose ball in the six yard box.
Osvaldo then put São Paulo 2-0 up after 38 minutes after being released by Cortez superbly turning the fullback inside out and coolly dinking the ball over the keeper.
Luís Fabiano then was bundled over for a penalty in the dying stages of the match, but failed to convert it as he smashed the ball onto the bar and over.
The game was marred by an injury to Lucas Moura who had to be stretchered off the pitch with a knee injury that may ruled him out of the game against Flamengo at the weekend.
São Paulo remain in fouth place while Atlético GO stay bottom of the Brasileirão.
