In the book, Jewel, now 41, writes that Penn sought her out with a phone call to her father's home in Alaska after watching her television debut on Conan O'Brien's show in 1995. Jewel's father, Atz Kilcher of Discovery's Alaska: The Last Frontier, assumed it was a prank call.
Penn asked the singer-songwriter if she would write a song for his upcoming film, The Crossing Guard. The pair would go on to meet and work together on the film before things became serious.
"He began to court me in earnest, following me around on tour, acting as my de facto roadie," she wrote. "I was nowhere near famous, opening for Peter Murphy of Bauhaus in small clubs."
Jewel would go on to cut the track "Emily" for the film, and accompany Penn to the Venice Film Festival. Still, tabloid reporters failed to notice the new relationship. (There is one photo of the couple together at the festival in the pages of Never Broken.)
"I kept our burgeoning relationship very quiet," she wrote. "I was determined not to be 'discovered' because I was dating someone in the public eye. I liked his mind, and I had fun sparring with him."
Jewel would walk the red carpet (solo, as a singer-songwriter for the film and not Penn's date), and dine with Hollywood heavyweights like Roman Polanski, Jack Nicholson and (later, back in Los Angeles) Warren Beatty.
"I enjoyed Sean and would eventually fall in love, but I did not go around holding hands or trying to be seen or noticed," she confessed.
The news comes just as Penn has filed a lawsuit against Lee Daniels for defamation, after the latter implied in an interview that the former had abused women.
The pair would eventually split, and Jewel would go on to marry cowboy Ty Murray in 2008. The couple announced that they would be divorcing after six years of marriage in 2014. Together they share one son, 4-year-old Kase.
Jewel opened up about her past with Penn in an interview with Howard Stern on Monday. Speaking about their breakup, she said: "It was hard on me. He really believed in me at a time when nobody else did. And he really made me feel good about myself and I was so desperate for that. Having that go away was hard."
In the same interview, Jewel referenced another bombshell from her book -- that Tupac Shakur had invited her to accompany him in Las Vegas on the weekend he was killed.
Jewel's book and new album, Picking Up the Pieces, a sequel to her 1995 debut, Pieces of You, are out now.