A spokesman for Brin and Anne Wojcicki confirmed to All Things Digital that "they have been living apart for several months. They remain good friends and partners."
The couple, both aged 40, have two children.
Brin's new girlfriend has been identified as Amanda Rosenberg - a former school friend of the Duchess of Cambridge.
Brin, who is the face of Google Glass, has a fortune believed to be worth around the $24bn, Forbes estimates.