Sgt. Heather Randol, a police spokeswoman, declined to discuss the circumstances that led to McDonald's arrest, saying only that officers had probable cause to take him into custody.
McDonald, 29, was later released from Santa Clara County Jail after posting $25,000 bail.
He wouldn't discuss what happened with television news reporters who approached him after he posted bail.
"I can't say too much, not right now, but the truth will come out. Everybody knows the kind of person that I am," McDonald said. "I'm a good-hearted person."
NFL Commissioner Roger Goodell announced tougher penalties this past week for players accused of domestic violence. The move followed scrutiny over Baltimore Ravens running back Ray Rice's two-game penalty stemming from his arrest on an assault charge in February.
"The 49ers organization is aware of the recent reports regarding Ray McDonald and we take such matters seriously," general manager Trent Baalke said in a statement. "As we continue to gather the facts, we will reserve further comment."
McDonald has been playing for San Francisco since he was drafted as a third-round pick in 2007.
The incident is the latest blow to what has been one of the NFL's fiercest defenses. On Friday, linebacker Aldon Smith received a nine-game suspension for what the league called violations of its substance-abuse and personal-conduct policies.
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