The 68-year-old singer and former PR woman Amanda Sheppard, 31, who married in a private ceremony on the Turks and Caicos Islands in 2011, were granted a decree nisi at London's High Court.
They now have to wait for a decree absolute to formally end the marriage in the coming weeks.
A statement from his Ferry's publicist said: "With great sadness, Amanda and Bryan have decided to go their separate ways.
"They remain on extremely good terms and wish each other only the best going forwards.
"They would each be extremely grateful if their privacy in regard to this matter could be respected."
This was the second marriage for the former Roxy Music frontman.
He was previously married to Lucy Helmore, with whom he has four children, for 21 years.
He also counts former model Jerry Hall as one of his ex-girlfriends.