An open letter from Allen was published online Friday night by The New York Times. In it, he blamed ex-girlfriend Mia Farrow for concocting the allegations.
"Of course, I did not molest Dylan," Allen wrote. "I loved her and hope one day she will grasp how she has been cheated out of having a loving father and exploited by a mother more interested in her own festering anger than her daughter's well-being."
Nearly a week ago, the Times released a letter from Dylan Farrow, claiming that in 1992, Allen sexually assaulted her.
In an overnight response to ABC News, Dylan Farrow made a point-by-point rebuttal of Allen's letter saying, "Woody Allen has an arsenal of lawyers and publicists but the one thing he does not have on his side is the truth."
The 78-year-old director was investigated for the alleged molestation, but was never charged. A team of child abuse specialists from the Yale-New Haven Hospital, brought in to the case by prosecutors and police, concluded that Dylan Farrow had not been molested.
At the time of the breakup of their 12-year relationship more than two decades ago, Mia Farrow first accused Allen of molesting Dylan Farrow. Allen has consistently denied the abuse allegation.
Their split followed the discovery of an affair between Allen and an adopted daughter of Mia Farrow, Soon-Yi Previn, when Previn was 19 or 21. (Her official date of birth is uncertain.) Allen and Previn married in 1997 and have two adopted daughters.
Allen said his open letter "will be my final word on this entire matter and no one will be responding on my behalf to any further comments on it by any party."
He ended the letter by saying, "Enough people have been hurt."
The Associated Press and ABC News contributed to this report.