San Jose police Sgt. Heather Randol says the 29-year-old defensive end was taken into custody early Sunday after officers responded to a home in an upscale neighborhood.
McDonald was jailed on felony domestic violence charges.
He has been playing for San Francisco since he was drafted as a third round pick in 2007.
NFL Commissioner Roger Goodell announced tougher penalties last week for players accused of domestic violence.
San Francisco 49ers General Manager Trent Baalke said in a statement Sunday that the team takes "such matters" seriously but is not commenting on the allegations involving McDonald without more information.