The governor's office said Johnathan Montgomery was released Tuesday night from the Greensville Correctional Center.
In issuing the conditional pardon, McDonnell called Montgomery's imprisonment a "travesty of justice."
The 26-year-old Montgomery was convicted in 2008 of sexually assaulting Elizabeth Paige Coast. Then 17, the accuser claimed Montgomery assaulted her outside her grandmother's house in Hampton in 2000 when he was 14 and she was 10. Montgomery was sentenced to 7 1/2 years in prison.
Since she recanted, Coast has been arrested on a perjury charge and released on bond.