"We are living separately and we are much happier this way," the pair told E! News.
"But we will always have much love and respect for each other. Even though we are separated, we will always remain best friends and, as always, our family will remain our number one priority."
The official statement comes just a week after Kris Jenner's younger sister "revealed the truth" behind her sibling's rocky relationship with Bruce Jenner.
Karen Houghton told In Touch magazine that Bruce has sought out a lawyer, despite the fact the couple "still do things together".
"[Kris and Bruce] are separated," she told the magazine.
"Their relationship goes back and forth. I would love to see them get back together."
The Jenners had been forced to deny rumours of a split for months, with reports the pair have been living separately - Bruce at the Kardashian beach house while his wife resides with the family at the Kardashian family home.
Houghton said her sister often gets herself into trouble for her flirty behaviour.
"I've heard she flirts with Scott [Disick, Kourtney's boyfriend] and Lamar [Odom, Khloé's husband] when she's drunk," she added.
Karen, who is known as "Crazy Auntie K" to her nieces and nephew said Kris has always been "generous and giving," despite at times being "crazy and controlling".
"She sent down a Mercedes for Valentine's Day. I went out front, and there was a big bow on it," reveals Karen, who is a part-time nurse and single mother to daughter Natalie Zettel, 15.
"She also furnished my whole house [in 2009]. A truck came down with $50,000 worth of furniture."
