The 89th minute goal allowed Santacruzense to snatch a 1-1 draw at home to Atletico Sorocaba in the Paulista Football Federation (FPF) Cup on Sunday, a regional tournament played in the state of Sao Paulo.
Pictures showed that after a Santacruzense player shot narrowly wide, the boy collected the ball with his feet and took it back on to the pitch.
However, instead of returning it to the goalkeeper, he subtly tapped it across the line into the net.
Although there was nearly 10 seconds between the shot going out and the boy placing the ball over the line, referee Silvia Regina de Oliveira awarded a goal amid furious Sorocaba protests.
Oliveira, who has refereed in the Brazilian first division and the Copa Sudamericana, said she based her decision on the linesman.
"I should have trusted my own vision," Oliveira said in a radio interview.
Marcos Marinho, head of the FPF's refereeing commission, said the goal would stand and the referee would face suspension.
"It was a very serious mistake and, unfortunately, the punishments will have to be applied for the referee and linesman," he said. "There was a lapse of concentration and that can't happen in football."