She also opens up about the “earth-shattering” moment when, she says, Jenner revealed a deeply held secret.
Thompson, 66, chatted with ABC News’ Chris Connelly about her book, “A Little Thing Called Life.”
“My happiness was complete until that day when Brody was 18 months old and Brandon was just about 3½,” she said, speaking of her sons with Jenner, “and my remarkable husband came to me one day and said, ‘I need to tell you something about myself.’”
Thompson said she feared Jenner was about to confess an affair.
“And he said, ‘I identify as a woman,’” she recalled. “He said, ‘I am a woman ... I would like to become female on the exterior, because I’ve always been female on the inside.’”
Watch the full interview on "Nightline" on Wednesday, Aug. 24 at 12:35 a.m. ET
“It was earth-shattering. It was devastating,” she said. “People can’t understand. ‘You must’ve had some kind of idea.’ No, nunca, nada, never, nothing.”
Therapy sessions brought her greater understanding, she said.
“My deeper compassion was for Bruce ... for her to have felt so trapped in the wrong body. It broke my heart to think that he, that he had struggled so long and so hard,” Thompson said.
While she struggled to understand the idea that her husband was transgender, she said, Jenner invited her to see him in New York. She anticipated a romantic weekend, but when she knocked on the door, Thompson said, Jenner appeared dressed in women’s clothing.
Thompson was unprepared and remembered that she “just crumbled.”
“I think I even fell down in the hall ... I just went, ‘Oh, oh, no, no.’ And I just started crying,” she said.
Thompson says Jenner, now 66, was contrite.
“‘I’m so sorry. I just thought it was very important that you see who I authentically am,’” she recalled Jenner saying to her. “Not until that moment, I guess, did it sink into my psyche that that truly was who Caitlyn felt that she was. And I had to respect that and honor that and move on with my life.”
The couple split in 1986. Thompson was Jenner’s second wife. Jenner married Kris Kardashian in 1991; they divorced in 2015.
After Jenner’s publicly announced transition last year, Thompson — a pageant standout who was Presley’s lover, confidante, confessor and caregiver for 4½ years, after his split from his wife, Priscilla Presley — was supportive.
“I think, more than anything, it’s been a relief for Caitlyn to be able to emerge as her true self. And we love her ... But when I first met her, she was in a Bruce Jenner body. He was just an incredible person. Still is,” she said.
She added, “I have since said to her, ‘You’ve got to give yourself credit. You know, you kicked manhood’s butt.’”
ABC News reached out to Jenner, but she wasn’t available for comment.