He replaces founders Chris DeWolfe and Tom Anderson who stepped down from the social networking site last week before their contracts were due to expire in October.
Van Natta will report directly to Jonathan Miller, News Corp's CEO of digital media and chief digital officer.
At Facebook Van Natta served as chief revenue officer and vice president of operations. He was closely involved in negotiating Facebook's $240m investment from Microsoft and focused on revenue operations, business development, strategic partnerships and technical operations.
Prior to joining Facebook he was vice president of worldwide business and corporate development for Amazon.com, where he managed global marketing programmes and strategic partnerships, while most recently, he was the CEO of online music company Playlist.
According to Miller: "Owen combines a deep understanding of social networking, a keen business sense and the operational experience to guide MySpace through its next phase of growth.
"I'm confident his leadership will be an invaluable asset."
Van Natta said: "I feel honoured to build upon the immeasurable achievements of the MySpace founders and look forward to working with Jon and the MySpace team to meet the challenges and make the most of the opportunities before us."
In addition to his other roles Van Natta was also part of the founding team of A9.com, the Amazon.com search company, and was responsible for site operations and sponsored-link advertising.
On leaving MySpace DeWolfe will continue to serve on the board of MySpace China and will act as a strategic advisor to News Corp.
His MySpace founding partner Anderson is currently in talks with Miller about taking on a new digital role within the company.