The San Francisco Chronicle reported that a 29-year-old man was arrested Sunday on suspicion of beating the 15-year-old boy for urinating in the man's car.
Reports of other assaults at the game were also logged with stadium security.
49ers' season ticket holder Daisy Barringer said she was kicked and punched by another 49ers fan.
The 36-year-old said she has seen violence at both home games this year, and during the preseason.
Security was increased at the stadium two years ago after two shootings, a beating and fights broke out during a preseason game with the Oakland Raiders.