The 34-year-old actress allegedly confessed the illicit affair to Marcheline Bertrand, causing irreparable damage to their relationship.
'Marcheline had a live-in boyfriend whom she was very much in love with, but Angie slept with him when she was 16 and barely out of school,' a source told Now magazine.
'Her mother found out and ended her relationship with the man.'
Shock claims: Angelina Jolie, pictured in Hollywood last night with partner Brad Pitt, allegedly slept with her mother's boyfriend as a teenager
Brushing off the scandal: Angelina made a sharp exit after dinner with her partner
Angelina was said to be devastated when her mother died of cancer, in 2007, at the age of 56.
The star is no stranger to scandal - she famously French-kissed her brother James Haven at the Oscars in 2000 and once sealed her love for former husband Billy Bob Thornton with a vial of blood.
She has since reinvented herself as a UN Goodwill Ambassador and a mother to three adopted children Maddox, 7, Pax, 5, Zahara, 4, and biological daughter, Shiloh, 3, and twins Vivienne and Knox, 15 months.
Morton, who has also written controversial unauthorised biographies on Tom Cruise and the late Princess Diana, is expected to release the book later this year.
'Damaged relationship': Angelina with her mother Marcheline Bertrand in 2001
He says: 'AJ is one of the most fascinating women on the planet. Hers has been an extraordinary journey and an extraordinary story. I'm looking forward to telling it.
Angelina, who last night dined at Hollywood Cicconi's restaurant with partner Brad Pitt, has not yet commented on the allegations.
A separate book, titled Brangelina Exposed, is also set to lift the lid on her relationship with Pitt.
It promises to explain how the famous couple 'have successfully manipulated the public into believing a glamorous fairytale that bears little resemblance to the reality of the pair's life together.'
Author Ian Halperin claims to reveal 'new details of her volatile relationship with and estrangement from her father Jon Voight, her struggles with suicidal impulses, her heroin use, her sexual exploits and her remarkable rise to become an Oscar-winning actress.'
