The San Jose University students, Logan Beaschler, 18, Joseph Bomgardner, 19 and Colin Warren, 18, decorated their apartment with a Confederate flag, Nazi symbols, photographs of Adolf Hitler and a white board with a racial slur.
They also nicknamed the student "Three-Fifths," a reference to the provision that counted slaves as three-fifths of a person.
The students have been charged with misdemeanor hate crime and battery, CNN reported, and they face a maximum of one year in county jail if they are convicted.
One of the students, Beaschler, was booked in Santa Clara County Jail Thursday and is being held in lieu of $15,000.
The unidentified 17-year-old victim suffered a minor injury when he removed the bike lock, police said.
"I can't believe in the year 2013 that we're talking about an African-American student being treated this way," District Attorney Jeffrey F. Rosen told CNN. "We're taking this case very seriously."
The students have been suspended from the university.