In a two-hour special
that aired Friday, the Olympic gold medalist and "Keeping Up With The Kardashians" star said he has the "soul of a female" even though he was born with male body parts.
Thompson, who had two sons with Jenner during their five-year marriage, was one of many relatives to cheer Jenner
for publicly sharing what she had known for decades.
"I have respectfully kept his secrets private and would have taken his confidences to my grave had he not spoken out," she said in a column for the Huffington Post
"He can finally realize his need to be who he authentically is, who he was born to be. That takes tremendous courage. For that I commend him."
Thompson wrote that she would not have married Jenner if she had known about his "gender issue" when they first met. But she's glad she didn't know because she would have missed the chance to share a life with him, including their two sons.
"Looking back, I'm so grateful to God, the universe, and Bruce that I didn't know, and that Bruce played the role in my life that he did," she said in the column.
The two met in 1979 at a celebrity tennis tournament at the Playboy Mansion, while Jenner was in the process of separating from his first wife. The two married on January 5, 1981, and made Hawaii their home. Their first son, Brandon, was born in 1981, followed by son Brody in 1983.
"The Bruce I knew back then was an easygoing, down-to-earth, casual, romantic, good and loving man. I was extremely happy to have found such a remarkable partner with whom to share my life. I found him to be honorable and, well, just too good to be true. Just too good to be true indeed," she wrote.
They were a celebrity "glamour couple" of the time, appearing regularly on red carpets, hosting charitable fundraisers and traveling the world together for their careers. Jenner's star grew, and was a man that other men aspired to be, and someone women wanted to be with.
"The Bruce I knew back then was unstudied, affable, and seemingly very comfortable in his own skin. So it seemed."
Thompson said Jenner told her in 1985 that, despite it all, "he identified as a woman" and hoped to move forward with the process of becoming a woman." Confused and desperate, Thompson suggested therapy to help her understand what he was going through and "determine if it was something we could overcome or 'fix.'"
"I was pretty ignorant of the fact that being transgender isn't something that can be overcome, fixed, prayed away, exorcised or obliterated by any other arcane notion," she said.
He considered traveling out of the country for gender-confirmation surgery and returning to the United States identifying as female, where his children could meet him as "Aunt Heather."
They separated after going to therapy for about six months and Jenner began taking female hormones and removing his hair through electrolysis. As he started developing breasts, his children began to notice -- a claim that Jenner also made in his interview.
Thompson says Jenner did not remain a presence in their lives after he married Kris Kardashian, mother of Kim, Khloe, Khourtney and Rob Kardashian. Together, the couple had two children, Kendall and Kylie.
Thompson said she forgives Jenner for those years. He has already "been held prisoner in his own flesh" and hopes that his life will get easier now.
In addition to "world's greatest athlete," she hopes people will remember him as "trailblazer for the civil rights of the transgender community."