Voight, star of The Champ and Ali, revealed that she no longer wanted to have anything to do with him.
Tomb Raider actress Jolie, 27, filed for divorce from Thornton in July, citing irreconcilable differences and seeking sole custody of their adopted son Maddox.
Voight told the Access Hollywood show that Jolie had "carried a lot of pain for years".
He also said he was "broken-hearted because I've been trying to reach my daughter and get her help, and I have failed and I'm sorry".
Unhealthy
Jolie issued a statement confirming that she was estranged from her father.
"I don't want to make public the reasons for my bad relationship with my father," she said.
"After all these years, I have determined that it is not healthy for me to be around my father, especially now that I am responsible for my own child."
Voight, who won an Oscar for his portrayal of a Vietnam veteran in Coming Home, added that his biggest sadness was not being able to see his grandson.
He and Jolie were reunited when they both worked on the film Tomb Raider but that they were no longer in contact.
Jolie and Thornton, 46, spent months seeking permission to adopt a Cambodian-born boy and to allow him into the US.
But months after baby Maddox was given permission to live in the US, Jolie and Thornton announced they had separated.
Devotion
The couple were known for their eccentricities such as wearing pendants filled with each other's blood.
But they had been thought of as a close couple and the news they had split came as a shock despite the fact both had previous failed marriages.
The Oscar-winning actress suggested that their separate careers and her devotion to their adopted child could have played a part in driving her and her husband apart.
Voight blamed his own separation from Jolie's mother Marcheline Bertrand for the problems with his daughter, having left the family home when she was just one year old.
Jolie won a best supporting actress Oscar for her role in Girl, Interrupted.
Thornton is also known as a writer, director, and musician. The two met on the set of the 1999 air traffic control comedy Pushing Tin.