Santa Clara County prosecutors filed the charges late Wednesday against Logan Beaschler and Colin Warren, both 18, and Joseph Bomgardner, 19. The young men each face up to a year in jail if convicted.
University President Mohammad Qayoumi said in a statement Thursday that the suspects have been suspended.
The victim, now 18, moved into the four-bedroom suite in August with seven other young men, all of whom are white. The harassment began after all the roommates had attended an orientation that included cultural sensitivity training, the San Jose Mercury News reported.
The victim's name was redacted from the police report, and the newspaper did not name him at his parents' request.
According to a university police report, the suspects admitted that they harassed the freshman but claimed they were merely playing "pranks" or "jokes."
At first, the suspects nicknamed the victim "Three-fifths" and "Fraction," referring to the way the U.S. government once counted a slave as three-fifths of a free person, police said. According to the incident report, they told investigators they also wrestled their roommate to the ground and placed a metal bicycle lock around his neck, and they blocked the victim's bedroom door with furniture several times to prevent him from coming out. They're also accused of writing a racial epithet on a dry-erase board in the suite's living room and hanging a Confederate flag in a window.
Investigators said they found Nazi symbols in the suite, including the "SS" lightning bolt symbol and a swastika, as well as pictures of pentagrams, apparently intended to alarm the victim, who is Christian.
The victim's parents had seen the Confederate flag and the epithet on the dry-erase board and reported it to housing officials. Two of the suspects were then transferred to a different dorm, the Mercury News reported.
Dorm staff were apparently aware even before the parents' report that the Confederate flag had been placed in a window and had asked the suspects to remove it so it was not visible to the public.
Beaschler declined to comment to the Mercury News, and efforts to reach the other two suspects were not successful. It was not clear whether they have retained lawyers.
Students at the university held a rally Thursday protesting the alleged hazing.
Qayoumi, SJSU's president, announced that the school will re-examine its diversity programs and campus housing safety measures.
"Diversity and a commitment to social justice are in SJSU's institutional DNA," he said Thursday, adding, "this deeply disturbing incident reaffirms that we must protect and steward our values."