The actress has agreed to keep details of the case sealed upon Pitt's request.
"There is little doubt that [Brad] would prefer to keep the entire case private, particularly given the detailed investigations by the Federal Bureau of Investigation and the Dept. of Children and Family Services into [the] allegation of abuse," state the court documents.
Jolie announced she was divorcing Pitt, citing irreconcilable differences, after an on-flight incident involving the actor and their son Maddox. She has been given sole custody of their six children, while he has been given "therapeutic visits".
Pitt was investigated by the FBI and Department of Children and Family Services, but concluded no further action was needed and he was not charged.
"It's nice to see that she has finally come around to supporting the sealing of documents weeks after he requested this action," a source told People. "Considering that both the FBI and child services thoroughly investigated this matter and cleared the father, this line of attack doesn't make much sense."
However, a second source says that while Pitt has been cleared in investigations, his treatment of the children has still left a lasting impact.
"They keep pointing to him being cleared," said the source. "While his behaviour didn't amount to anything criminal, that doesn't mean he didn't do anything wrong. The kids are traumatised. The mum has been protecting the kids by not revealing what really happened on that plane. Her interest since the outset hasn't changed: to protect the health and safety of the kids."
In December, Pitt accused Jolie of releasing private information about their children through court filings, asserting that she has "no self-regulating mechanism". Jolie denied the claims.