Bay City News said team officials confirmed it Saturday afternoon.
"The San Francisco 49ers are aware that Aldon Smith incurred minor injuries during an incident last night," said General Manager Trent Baalke in a statement.
"We are in contact with Aldon, and thankful that his injuries were not more serious and that he is recovering comfortably," Baalke said. "The 49ers are also in communication with local authorities as they gather information regarding the incident, and will reserve further comment at this time."
Smith's injury has been linked in published reports to a house party in the hills east of San Jose early this morning that resulted in a shooting and stabbing.
Santa Clara County emergency dispatchers received a 911 call at 2:14 a.m. from someone reporting hearing gunshots coming from a home in the 4000 block of Higuera Highland Lane, sheriff's spokesman Jose Cardoza said.
A large party was being held in the home, and Sheriff's deputies found a crowd of at least 100 people when they responded, Cardoza said.
They located two gunshot victims and one stabbing victim, and took them all to area hospitals. All three victims were expected to survive, Cardoza said.
The scene was "kind of chaotic," and deputies are still working to determine what happened. No arrest have been made in the case.
Anyone with information on the case is asked to call sheriff's investigators at (408) 808-4500. Those wishing to remain anonymous can call (408) 808-4431.
ABC7 News contributed to this report.