The elegant playmaker, whose career started promisingly but has since been blighted by injuries, was pelted with "a shower of coins" when he took a corner and as he left the pitch, the Sao Paulo Tribunal for Sporting Justice (TJD/SP) said.
Santos' representative Joao Gazola played down the incident during their 3-1 win at Vila Belmiro on Feb. 3.
"Nobody wanted to hurt the player," he said. "It was a protest by a few people. The coins symbolised discontent, that was all. I hope he is happy at Sao Paulo but Santos are much greater."
Ganso's move to Sao Paulo last year was seen as betrayal by Santos fans, who had expected him either to stay at the club or go to Europe.
He was also pelted with coins by Santos fans at a match last year when he was still playing for the club after it emerged that he had been negotiating with Sao Paulo.
Ganso was initially seen as a player who could lead Brazil at the 2014 World Cup until his progress was hampered by injuries.