The deal was voluntary and doesn't reflect any ruling from the court regarding permanent custody, legal or physical, the source said.
Both Pitt and Jolie agreed to receive individual counseling, the source said, and Pitt offered to submit to drug and alcohol testing, which was not required.
The couple agreed that Pitt's first visit with the children would include a therapist, but there was no requirement for a monitor during subsequent visits, the source said. However, a second person close to the situation said the presence of a therapist was required at all visits for the duration of the agreement, which runs though Oct. 20.
At that point, the Los Angeles County Department of Children and Family Services will reevaluate the situation, the second person said, adding that until then, Jolie has custody and Pitt has visitation.
Decision-making for Maddox, 15; Pax, 12; Zahara, 11; Shiloh, 10; and 8-year-old twins Knox and Vivienne will follow a structured plan agreed to by both parents.
The "Maleficent" actress filed for divorce from the "World War Z" actor on Sept. 19, giving their date of separation as Sept. 15. Child and Family Services has been investigating an incident alleged to have happened Sept. 14 between Pitt and Maddox on a private plane bound from France to L.A. The FBI was also informed of the alleged incident, which sources said was physical but didn't involve punching or hitting.
Jolie attorney Robert Offer told the Associated Press last week that her decision to divorce had been made "for the health of the family."
"I'm currently focused on my family situation and don't want to distract attention away from this extraordinary film," Pitt said Tuesday in a statement announcing that he would be skipping the Wednesday premiere of Terrence Malick's "Voyage of Time," which he narrates.
Follow Christie D'Zurilla on Twitter @theCDZ.
3:05 p.m.: This article was updated with additional details regarding the terms of the agreement.