Stellenbosch University said in a statement that disciplinary proceedings found that undergraduate student Theuns du Toit was in the wrong and "there is no alternative but to expel" him with immediate effect.
"The university takes a zero-tolerance approach to racism, discrimination, prejudice and conduct which assails the dignity of another person," deputy vice chancellor Deresh Ramjugernath said in the statement.
The humiliation of the Black student in May stirred outrage in a country still battling deep divisions 28 years after the end of white-minority rule.
President Cyril Ramaphosa said the incident showed that racism still blighted "everyday life in South Africa".
The viral video showed a first-year white student urinating on the books and laptop belonging to a Black colleague in the early hours of May 15.
Justice Minister Ronald Lamola denounced the incident as "akin to urinating on the Constitution itself."