The students rushed the stage Monday after a news conference held by the university and NAACP leaders, the San Jose Mercury News reported.
"Last semester when we were protesting and requesting to meet with you, we were trying our hardest to let you know that something was terribly wrong with the experience that African-American students are having at San Jose State," Gary Daniels, an SJSU student and chairman of the Black Unity Group, told school President Mo Qayoumi. "But you did not want to hear us."
The press conference was held hours after Qayoumi took personal responsibility for the alleged abuse of a black student by his white roommates.
"By failing to recognize the meaning of a Confederate flag, intervene earlier to stop the abuse or impose sanctions as soon as the gravity of the behavior became clear, we failed him. I failed him," Qayoumi said in a statement released Monday.
The students hung a Confederate flag in the room, put a bicycle lock around his neck and called him names, the Mercury News reported.
Qayoumi said an independent expert will investigate the university's actions and propose reforms.
NAACP officials also said at the press conference the accused students -- Joseph Bomgardner, 19, Logan Beaschler, 18, Colin Warren, 18, and another minor who is not being named -- should have been charged with felonies, not misdemeanors.