General manager Trent Baalke announced the move during a Wednesday news conference at the 49ers' facility. Baalke cited a "pattern of behavior" in the team's decision to cut ties with the former third-round pick.
"I can say that we have had multiple discussions with Ray over time and there's been things that have been discussed with him," Baalke said. "And there was a plan that was put in place and this is a situation that has gone against that plan."
According to police, the woman connected with the investigation told police she was "possibly" sexually assaulted by McDonald, who has had several run-ins with the law since entering the NFL in 2007. No arrests have been made in the current investigation and no charges have been filed.
When reached by NFL Media, an NFL spokesperson said the league is looking into the matter.
McDonald was arrested in late August on suspicion of committing domestic violence against his fiancée. In November, the Santa Clara District Attorney's office declined to press charges due to insufficient evidence.
The 49ers drew criticism for standing by McDonald as the domestic violence investigation played out. The team obviously decided to take a different road in light of the new allegations.