The allegation was contained in a civil lawsuit filed Tuesday in Santa Clara County against Brooks and McDonald.
The woman says she slipped and fell on a pool deck at McDonald's house in December 2014 and continued to fall after that due to her initial head injury and alcohol consumption. McDonald initially thought she was dead, but did not call 911, telling others he didn't want a dead female found on his property, according to the suit.
At some point, Brooks groped her before McDonald carried her upstairs to his bedroom and sexually assaulted her, the lawsuit claims.
The woman says she believes surveillance footage will corroborate her allegations against Brooks and show McDonald carrying her upstairs.
McDonald has sued the woman for defamation, saying security camera footage would show a consensual sexual encounter occurred in his hot tub. A call to McDonald's attorney seeking comment on the allegation was not returned Wednesday.
Gregory Williams, Brooks' agent, said he was just learning of the allegations and did not immediately have a comment Wednesday.
The 49ers cut McDonald in December after learning of the allegation. The Santa Clara County district attorney is considering whether to file criminal charges against him.
Prosecutors are including Ahmad Brooks in their review, said Sean Webby, a spokesman for the district attorney's office.
The 49ers have experienced a rash of off-the-field incidents and arrests in recent years. Team CEO Jed York said after the team parted ways with coach Jim Harbaugh in December that he wanted to return the 49ers to winning with class.
In a statement, 49ers general manager Trent Baalke said the team was aware of the media report regarding Brooks. "We were disappointed to learn of this matter and will continue to monitor the situation," Baalke said in the statement.