The official, who spoke on condition of anonymity because the investigation was ongoing, said that if the district attorney's office files a case against the men, the man previously identified as the suspect, Giovanni Ramirez, would be exonerated.
The arrest marks a dramatic turn in the case. Since Giovanni was arrested May 22, police have consistently restated they believed they had their man.
"I'm happy for my client. I always believed he was factually innocent," Ramirez attorney Anthony Brooklier told the Los Angeles Times. "There was a lot of pressure on LAPD. I believe that they were operating in good faith and made a good faith mistake."
Giants fan Bryan Stow was almost fatally beaten outside the stadium after attending the March 31 season opener between the Giants and archrival Los Angeles Dodgers.
A paramedic and father of two, the 42-year-old Stow was transported from Los Angeles to San Francisco in May after being in a coma and in critical condition for months before doctors upgraded his condition to serious in June.
Ramirez, a convicted felon, is in prison for a parole violation after police found a gun in the house where he was staying when he was arrested.