Reports suggest at least two fans were attacked after the 0-0 draw between the local rivals in the Paulista A1 on Sunday and that a 34-year-old died.
Santos confirmed the incident on Monday, offering their condolences to the families of the two victims.
"Santos FC deplores the acts of violence that unfortunately made two more victims, including fatal, last Sunday after playing at Morumbi," the club said in a statement.
"The club has always maintained a culture of peace, and believes this is an essential condition for the development of world football, offers its condolences to the families of the fans involved."
The incident is just the latest crowd trouble in Brazil, who will host the World Cup starting June 12, with at least 30 fans killed last year.
