Anthony Broadwater, 61, was convicted and jailed the following year for attacking Ms Sebold when she was an 18-year-old student at Syracuse University.
His the conviction was overturned last week by prosecutors who determined his arrest and trial were seriously flawed.
In a public letter to Mr Broadwater, Ms Sebold said she was truly sorry for what he had gone through.
The 58-year-old wrote: “As a traumatized 18-year-old rape victim, I chose to trust the American justice system.
“My goal in 1982 was justice – not to perpetuate injustice. And certainly not to forever and irreparably change the life of a young man by the very crime that had changed mine. “
She added: “I am especially sorry that the life you could have lived was unfairly stolen from you, and I know that no excuse can change what happened to you and never will…
“I will continue to fight the role I unwittingly played in a system that sent an innocent person to prison. “
In a statement released by his lawyers, Mr Broadwater said he was “relieved that she apologized”.
He continued, “It must have taken a lot of courage for him to do that.
“It is still painful for me because I was wrongly convicted, but it will help me in my process to make peace with what happened. “
According to Variety, studio executives have canceled an upcoming film based on Ms. Sebold’s book Lucky, which details how she was raped and beaten in a tunnel near her college campus.
The 1999 book describes how Ms Sebold spotted a black man on the street several months after the incident she believed to be her attacker.
When she went to police, an officer said the man must have been Mr. Broadwater, who was allegedly seen in the area. He receives the pseudonym Gregory Madison in the book.
After Mr Broadwater’s arrest, Ms Sebold failed to identify him in a police queue, choosing another man as her attacker because she was afraid of “the expression in her eyes. eyes “.
But prosecutors still tried Mr. Broadwater.
He was convicted in large part because Ms Sebold had identified him as her rapist on the witness stand and testified that the microscopic analysis of the hair linked him to the crime.
This type of analysis has since been discredited by the US Department of Justice.
Mr Broadwater, who was released from jail in 1998, told The Associated Press last week he was crying “tears of joy and relief” after his conviction was overturned by a Syracuse judge.
Publisher Simon & Schuster and its Scribner imprint said on Tuesday they had ceased distribution of Lucky in all formats and were working with the author to consider how it could be revised.
Ms Sebold, who is also known for her books The Lovely Bones and The Almost Moon, added in her statement: “I am grateful that Mr. Broadwater has finally been vindicated, but the fact remains that there is 40 years old, he has become another young black man brutalized by our flawed legal system.
“I will always be sorry for what was done to him. ”