The couple founded MJM International together in 1996 and had been in dispute over who should take ownership following their split in 2011.
The 41-year-old Scots businesswoman said she was delighted the process was at an end after a difficult year.
A joint statement from the couple said: "We are both saddened that our marriage has broken down; however, we are pleased to confirm that we have reached an amicable agreement on all matters.
"We wish each other all the best as we embark upon the next chapter of our lives and, as parents, are committed to continuing to work together in the best interests of our children."
Ms Mone added: "I'm delighted after a tough year this has all come to an end. Michael has left Ultimo today. My focus is my children and growing Ultimo to the next level."
The pair broke up after 19 years of marriage amid allegations Mr Mone was having an affair with an Ultimo colleague – a claim he has denied.
The Mones have three children together – Rebecca, 19, Declan, 15, and Bethany, 11.
Ms Mone is understood to have held 142 shares in parent firm MJM International while her husband had one more with 143. However, the details of her takeover remain unclear.
Speaking after their separation, Ms Mone claimed she could no longer work with her ex-partner.