All six of their children Maddox Jolie-Pitt, 15, Pax Jolie-Pitt, 12, Zahara Jolie-Pitt, 11, Shiloh Jolie-Pitt, 10, and twins Knox Jolie-Pitt and Vivienne Jolie-Pitt, 8 will remain in Jolie's custody, reported E! online.
"We can confirm that childcare professionals have encouraged a legal agreement accepted and signed by both sides over a week ago," a representative for the actress said in a statement.
"In accordance with this agreement, the six children will stay in their mother's custody, and the children will continue therapeutic visits with their father. This has been determined by childcare professionals to be in the children's best interest."
The statement continued, "We are not in a position to discuss the details. We hope now that it is clear that the events which led to the dissolution filing involved minor children and their well being, there will be understanding of the sensitivity of the family situation. We believe that all sides are committed to healing the family and ask for your consideration during this difficult time."
Last Friday, Pitt filed for joint custody of the former couple's children as Jolie, 41, asked for sole custody at the time of the divorce announcement back in mid-September.
The 52-year-old actor has been under investigation over a mid-air altercation on a private aircraft September 14 with son Maddox.
The alleged incident prompted an anonymous call to the Los Angeles County Department of Children and Family Services over claims that the "Allied" star had been both physically and verbally abusive towards the teen.
Pitt has seen his kids twice since Angelina filed for divorce, and Maddox for the first time just recently.
Pitt and Jolie married back in 2014 and were first romantically linked back in 2004.
This marks the second divorce for Pitt, who was previously married to Jennifer Aniston, and the third divorce for Jolie, who was also married to Billy Bob Thornton and Jonny Lee Miller.