"After living apart for some time, we have made the difficult decision to separate as a couple amicably," they said in a statement issued to The Australian's Media Diary.
"With the greatest of respect for each other, we’ve come to the mutual conclusion that this is the best course for us to take while committed to the co-parenting of our daughter."
The news comes just hours after PE Nation founder Pip Edwards denied any involvement in their shock uncoupling.
Pip and Michael confirmed to Daily Mail Australia the two have been close friends for 12 years and are working on a project together.
"Absolutely unfounded and untrue. That's all I have to say. Thank you," Pip said.
Meanwhile, Michael Clarke's personal assistant Sasha Armstrong, who he was seen getting close to on a yacht, added: "Michael has known Pip for over a decade and is currently working with both Pip and Claire [Treg - PE Nation's co-founder] on a special project with P.E Nation."
It is believed that the couple split five months ago, with Michael moving out of their $12 million mansion in Vaucluse and into their $8million home on Bondi's beachfront.