In a lawsuit over a French winery that the stars bought, Ms Jolie says Mr Pitt grabbed her by the head and attacked two of their children on the 2016 trip.
Mr Pitt also verbally abused and poured alcohol on his family during the flight from France to Los Angeles, she says.
He denies the allegations.
Ms Jolie’s claim of abusive behaviour by Mr Pitt on the 14 September 2016 flight has emerged in previous court papers, including the Oscar-winning former couple’s divorce settlement.
But new details were alleged in Tuesday’s filing in Los Angeles by Ms Jolie’s legal team. It is part of an ongoing lawsuit over Chateau Miraval SA, a home and vineyard in the south of France that the former Hollywood couple acquired together.
Mr Pitt argues that he and his former wife had agreed not to sell their stakes in the venue without the permission of the other.
Ms Jolie disputes this, and blames Mr Pitt for ending negotiations over purchasing her shares of the property.
Her cross-complaint on Tuesday says the actor was physically and emotionally abusive towards her and their six children – aged 8 to 15 at the time – during the private plane flight.
Her lawyers allege the Fight Club star began shouting, accusing her of being “too deferential to the children”.
Shortly into the flight, Mr Pitt “pulled her into the bathroom” in the back of the plane, says the lawsuit.
“Pitt grabbed Jolie by the head and shook her, and then grabbed her shoulders and shook her again before pushing her into the bathroom wall,” the filing adds.
“Pitt then punched the ceiling of the plane numerous times, prompting Jolie to leave the bathroom.”
After one child verbally intervened, Mr Pitt “lunged at his own child”, says the filing.
Ms Jolie then “grabbed him from behind to stop him”, according to the court papers.
“To get Jolie off his back, Pitt threw himself backwards into the airplane’s seats injuring Jolie’s back and elbow,” the legal filing continues.