Vasco fans attempted to stone the Sao Paulo bus as it arrive at their Sao Januario stadium and there was also a row between officials when the visitors were initially banned from warming up on the pitch.
Brazilian media also said the visitors found their dressing-room door locked when they arrived and had to force it open.
"We just want to give Sao Paulo the same treatment that everyone receives in all the stadiums," said Vasco president Roberto Dinamite.
Midfielder Jorge Wagner gave Sao Paulo the lead in the 21st minute when he found the top corner with a free kick from the edge of the area.
Madson rifled in a long-range shot to equalise nine minutes later but Sao Paulo regained the lead at the start of the second half when Hugo scored following a corner.
The defeat left former South American champions Vasco da Gama rooted in the relegation zone with two matches to play.
Sao Paulo increased their lead at the top to five points over Gremio, who lost 4-2 at Vitoria, and need only one more win to clinch the title.
Cruzeiro went third with a controversial 3-2 win over Flamengo.
Fernandinho and Thiago Ribeiro twice put Cruzeiro ahead but Ibson and Obina replied each time to set up a stormy finale.
Ramires fired the winner from the edge of the area in the 84th minute while the visitors were furious after having a penalty appeal turned down in the last minute.
Diego Tardelli was sent off for dissent and captain Fabio Luciano followed after the final whistle as the protests continued.
