A person with knowledge of the situation told The Associated Press that Smith suffered stab wounds. The person spoke on condition of anonymity Saturday because those details had not been released.
"(We) are aware that Aldon Smith incurred minor injuries during an incident last night," the 49ers said in a statement. "We are in contact with Aldon and thankful that his injuries were not more serious and that he is recovering comfortably. The 49ers are also in communication with local authorities as they gather information regarding the incident, and will reserve further comment at this time."
According to The Sacramento Bee, deputies from the Santa Clara County sheriff's office were called to a house party at about 2 a.m. on Saturday after receiving reports of gunshots. When police arrived, they found two people shot and another stabbed.
The Bee reported that all three were taken to the hospital with what were believed to be non-life-threatening injuries.
A source told the Bee the stabbing victim was Smith. A spokesman for the Santa Clara County sheriff's department, meanwhile, would not comment on the identity of the victims.
The party was so large -- more than 100 people were estimated to be there -- that deputies called for backup from the San Jose police and the California Highway Patrol, Sgt. Jose Cardoza told the Bee.
"It was a chaotic scene," Cardoza said. "There was a lot of commotion, and no one knows where the gunshots came from."
Cardoza told the newspaper there are no suspects in the case at this time.
In January, Smith was charged with driving under the influence in Miami Beach.
Smith, 22, made a franchise-rookie record 14 sacks, most among NFL rookies, last season, to go along with two forced fumbles.
The 6-foot-4, 258-pound Smith was the seventh overall pick in the 2011 NFL draft out of Missouri.
Information from The Associated Press was used in this report.