According to ESPN, the team said they are warning fans that they will not tolerate rowdy behavior.
Also, team CEO Jed York wants the NFL to call off the annual preseason battle between the Niners and Raiders indefinitely.
"This is a game where you have a rivalry situation and, unfortunately you have the worst segment from a very small segment of both fan bases that come and brings about this type of event," York said at a news conference at Candlestick Park. "It's our belief that we should recommend to the NFL that this game is at least postponed for some period of time."
In response, Raiders' CEO Amy Trask said: "We have a terrific working relationship with the 49ers organization, and we look forward to discussing and addressing this issue with them, in the same collaborative and cooperative manner we do all issues."
Despite the 49ers 17-3 win over the Raiders, it was overshadowed by the violence.
As a result of the violence, two men were initially listed as seriously injured, but their condition were upgraded to fair condition on Monday.
One of the victims, a 24-year-old man, was shot several times in the stomach. Police said he managed to make it to stadium security for help despite the injuries. The other, a 26-year-old man, was beaten unconscious in an upper level stadium restroom during the fourth quarter. Yet another shooting victim was treated, after receiving superficial facial wounds after the game.
No arrests have been made.
During the chaos, police ejected at least 70 people from the stadium on Saturday (August 20). Additionally, there were 90 calls for medical service that day, a figure far higher than at a typical Niners home game, officials said.
Due to the madness, Police Chief Greg Suhr, Mayor Ed Lee and 49ers team officials will place DUI checkpoints near the stadium after games to stop alcohol consumption. They also plan to make police and security more visible inside and outside the stadium, and urged fans to be more accountable for their actions.
"To those of you who decide to come to our games, and it really doesn't matter what jersey you may be wearing, or what hat you may wear, or what team you may support, your behavior on Saturday night is not welcome," said Jim Mercurio, the 49ers' vice president of stadium operations and security. "Don't come here. You're not welcome."