The 78-year-old filmmaker says Dylan Farrow's open letter published last week includes "creative flourishes that seem to have magically appeared during our 21-year estrangement".
At the time of the break-up of their 12-year relationship more than two decades ago, Mia Farrow accused Allen of molesting Dylan. Allen has consistently denied the abuse allegation.
Allen claims in his letter that seven-year-old Dylan was coached by Mia Farrow.
Dylan Farrow claimed in her open letter that Allen abused her in 1992 at the family's Connecticut home.
Allen said his letter will be his final word on the matter.
"Of course, I did not molest Dylan," writes Allen.
"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."
Allen 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.
"Now it's 21 years later and Dylan has come forward with the accusations that the Yale experts investigated and found false," Allen said.
His split with Mia Farrow followed the discovery of an affair between Allen and Mia Farrow's adopted daughter, Soon-Yi Previn, when she was 19 or 21. (Her official date of birth is uncertain.)
Allen and Previn married in 1997 and have two adopted daughters.
"I still loved (Dylan) deeply, and felt guilty that by falling in love with Soon-Yi I had put her in the position of being used as a pawn for revenge," Allen said.
"Not that I doubt Dylan hasn't come to believe she's been molested, but if from the age of seven a vulnerable child is taught by a strong mother to hate her father because he is a monster who abused her, is it so inconceivable that after many years of this indoctrination the image of me Mia wanted to establish had taken root?"
The 28-year-old Dylan Farrow, now married, currently lives in Florida under another name. Her letter caused an uproar, reawakening a case more than two decades after it made headlines.
Some have challenged her account, most notably her 36-year-old brother, Moses Farrow. He told People magazine this week that "of course" Allen did not molest Dylan Farrow, which she called "a betrayal".