The shootings occurred around 8 p.m. PT, shortly after the 49ers' 17-3 victory, police Sgt. Michael Andraychak said.
The victims are a 24-year-old man, who was hospitalized with life-threatening injuries, and a 20-year-old man, who was hospitalized and was expected to survive, Andraychak said. Their names have not been released.
The Chronicle reports that the 24-year-old victim was wearing an "(expletive) the 49ers" T-shirt. He was in critical condition with two to four gunshot wounds to the stomach Saturday night at San Francisco General Hospital, according to the newspaper.
The 20-year-old victim was discovered near Pole V in the Candlestick lot, suffering from superficial wounds to the face, according to the newspaper. He was in stable condition at the hospital.
"We are treating it as separate shootings, but we believe they are related," Harrell said.
The two victims and the suspect had all attended the game, Harrell said.
The Chronicle also reported that a third man, a 26-year-old from San Rafael, Calif., was hospitalized with life-threatening injuries after he was assaulted and knocked unconscious in a restroom at Candlestick during the game, according to police.
Police said a suspect was arrested.
The Chronicle reported that police had yet to establish a link between the shootings.
The 49ers issued a statement acknowledging the shootings and the investigation, but offering no further details.
The violence was not the first involving a San Francisco sports team's game this year.
In March, San Francisco Giants fan Bryan Stow was severely beaten by two men in Los Angeles Dodgers gear outside Dodger Stadium after the teams' season opener. He remains in a San Francisco hospital in serious condition with brain injuries. Two suspects have been charged in the case.
The Associated Press contributed to this report.