The young man was assaulted at the weekend on the platform of the city centre's Nevksy Prospect metro station by fans from the local Zenit football club, who were fighting among themselves, police said on Wednesday.
A 20-year-old Russian was arrested in the course of the police inquiry.
The student, named as Abdou-al-Kaader Mamoun Bedeoui, was in his first year at a technical university in Saint Petersburg, according to Syrian diplomatic sources.
The Syrian's death comes amid increasing racial attacks in the former imperial capital that considers itself Russia's liberal intellectual heart.
At the beginning of February, police blamed skinheads for the death by stabbing of a nine-year-old Tajik girl as she walked home with her father and cousin who were also injured.
In recent years, xenophobic attacks have occurred regularly in major Russian cities, usually targeting African and Asian students, as well as diplomats and traders from Central Asia and the Caucasus region.