Detectives searched McDonald's home on Tuesday, San Jose police Sgt. Heather Randol said Wednesday.
The 49ers responded by releasing the seven-year player. General Manager Trent Baalke said he informed McDonald and his agent of the decision by phone at 11:30 a.m. Wednesday.
A hospital notified police Tuesday morning that a woman was seeking treatment, Randol said. The police say the woman told them she was "possibly" sexually assaulted by McDonald. There have been no arrests or charges filed.
McDonald was accused of hitting his pregnant fiancee in August. The Santa Clara County district attorney decided last month not to file charges against him because of a lack of evidence.
The 49ers had allowed him to play while that investigation took place, a decision considered to be controversial in the aftermath of the Ray Rice domestic abuse scandal the NFL has been dealing with this season.
Calling it a "team decision" to let McDonald go at this time, Baalke said Chief Executive Jed York and Coach Jim Harbaugh were also involved and that the 49ers also notified the NFL of McDonald's situation.
“This is a situation that we can all learn from,” Baalke said.