McDonald is being investigated by authorities for an alleged sexual assault that took place at his home earlier this week.
"While this organization has a strong belief in due process and has demonstrated that over time, Ray’s demonstrated a pattern of poor decision making that has led to multiple distractions to this organization and this football team that really can no longer be tolerated. And that’s the reason for the decision we made today," general manager Trent Baalke said in a press conference Wednesday.
Tuesday, police served a search warrant for McDonald's home after a possible sexual assault victim notified police from a local hospital. "The preliminary investigation revealed the alleged suspect was Ray McDonald," San Jose police spokeswoman Sgt. Heather Randol wrote in an e-mail to the San Jose Mercury News.
No arrests have been made and the investigation is ongoing.
Last month, the Santa Clara County District Attorney's office elected not to charge McDonald in a domestic violence case stemming from an incident at his home involving a pregnant woman Aug. 31, a week prior to San Francisco's first regular season game.
Prosecutors cited conflicting versions of what happened, a lack of verifiable eyewitnesses and a lack of cooperation by the alleged victim, McDonald's fiancee.
"This isn’t about this one incident. This is about a pattern," Baalke said. "If this was one incident we would be standing up here talking about due process like we have multiple times in multiple other situations."
The 49ers allowed McDonald to play during the investigation despite far-reaching criticism to keep him off the field. He has not missed a start in 14 games this season with head coach Jim Harbaugh, CEO Jed York and Baalke all going on the record stating the organization would rely on due process in McDonald's case before making any disciplinary decisions.
"I'm not the kind of guy to put a hand on a woman like that," McDonald said after being exonerated in November. "I respect women and the truth came out. It was weighing on me because a lot of things were being said about me that I knew weren't true. I just kept my mouth shut and let the process play out."
A security video at a local hotel captured McDonald and teammate Brandon Lloyd breaking up a fight at a bar the night of Dec. 5, two days before the 49ers played the Oakland Raiders. Baalke said the organization was aware of the incident after video had been leaked by TMZ Sports.
"And (we) certainly took a look at that, and, as you know, that was more them stepping in and defending in that situation. But all of it adds up. And I’ll leave it at that," Baalke said.
Along with the incident in August, police were reportedly called to McDonald's home in May after an altercation involved a woman brandishing a gun. She left the home after the man involved threatened to call the police. The police spoke to both parties involved and did not say which party called authorities. The police initially released the report because of "overwhelming media interest" after McDonald was being investigated for August's domestic violence case.
This week's investigation centering around McDonald marks his third since May. He was also arrested for a DUI in June of 2010.
"We expect a lot from our players, hold them accountable for their actions," Baalke said. "And when it becomes a pattern of poor decision making, this can, and will be the result."
McDonald was signed by San Francisco through 2018 and reportedly had $17.1 million in base salary remaining on his contract.