After examining information submitted by police, District Attorney George Gascon said his office determined that no charges would be filed "at this time."
"The San Francisco Police Department - Special Victims Unit completed and submitted a thorough investigation of the allegations against Michael Crabtree," Gascon said.
Crabtree's attorney, Joshua Bentley, didn't immediately return a call seeking comment.
San Francisco police said Crabtree was never detained or arrested in the matter, and that he co-operated fully with their investigation.
The 49ers are preparing to meet the Baltimore Ravens in the Super Bowl on Feb. 3 in New Orleans.
49ers general manager Trent Baalke said the team was pleased that the district attorney decided to not file charges after reviewing the matter.
"Michael and the team can now put this behind us and move forward," Baalke said in a statement.
During the regular season, Crabtree became the first San Francisco wide receiver with more than 1,000 yards in a season since Terrell Owens in 2003.