Parker was charged with rape while a student at Penn State in 1999. He was acquitted, and the accuser committed suicide in 2012 at the age of 30.
Late Tuesday, Parker took to Facebook to express his feelings "from my heart and not filtered through a third party gaze."
"Over the last several days, a part of my past -- my arrest, trial and acquittal on charges of sexual assault -- has become a focal point for media coverage, social media speculation and industry conversation," said Parker, who characterized himself as "devastated." "I understand why so many are concerned and rightfully have questions."
Parker said he had only recently learned of the death of his accuser. In speaking with the media, her family has said the trauma of the rape contributed to her death.
The director said in his Facebook statement that he did not want to "ignore the pain she endured during and following our trial."
"While I maintain my innocence that the encounter was unambiguously consensual, there are things more important than the law," he wrote. "There is morality; no one who calls himself a man of faith should even be in that situation."
Parker and his college roomate Jean Celestin, who co-wrote "Birth of a Nation," were accused of raping a then-18-year-old student while she was drunk. Celestin was convicted at a trial in 2001, but his conviction was later reversed on appeal.
In an email to Deadline, Celestin wrote, "This was something that I experienced as a college student 17 years ago and was fully exonerated of."
"I have since moved on and been focusing on my family and writing career," Celestin said. "I have several exciting book and film projects that I am working on and that I am looking forward to."
Parker was asked by Variety and called the case a "very painful moment in my life." He reiterated that he was acquitted and said he is now a family man with a wife and five daughters.
"I can't relive 17 years ago," Parker said. "All I can do is be the best man I can be now."
"Birth of a Nation," a drama about Nat Turner's slave rebellion in 1831, is set to open on October 7.