Martin died of breast cancer at 1:50 a.m., her husband Ron told the website.
Martin is the younger sister of Jolie's mother, actress Marcheline Bertrand, who died of ovarian cancer in 2006, at age 56. Jolie's maternal grandmother also died of ovarian cancer, at 45.
Bertrand's famous ex-husband and Jolie's father, Jon Voight, was said to be spending time with Martin in her final days, as was Jolie.
Jolie pre-emptively had a double mastectomy in February due to her genetic predisposition to breast cancer. She wrote about her experience in a New York Times article.
It led others to speak about the condition, including CNN anchor Zoraida Sambolin who also revealed she had a double mastectomy after learning she had breast cancer. Time magazine May 27's cover story is titled "The Angelina Effect."
"We have seen Angelina a number of times since Debbie was diagnosed with breast cancer," Martin told the website of his late wife. "Debbie and I were both very proud of her recent decision to have the double mastectomy, and to do everything she can to keep her family from having to go through what we've been through."