Kris confirmed the news to Us magazine, saying, "I will always love him."
"We are living apart. But there is no animosity. We are united and committed to our family," Kris said.
The estranged couple remain on good terms and have no plan to divorce any time soon.
"We ended a marriage, but that's not the end of our friendship. I will always love him, but we are longer a couple in that way," she added.
Married since 1991, Kris and Bruce have two kids together, daughters Kendall, 17, and Kylie, 16. Kris is also a mother to Kourtney, 34, Kim, 32, Khloe, 29, and Rob, 26, with first husband Robert Kardashian, who died in 2003.
"We are happier this way," Kris said of the split, which she and her family kept secret for a year.