In the document, Jolie Pitt filed for physical custody of the couple's six children and cited irreconcilable differences.
"This decision was made for the health of the family. She will not be commenting at this time, and asks that the family be given their privacy during this difficult time," Jolie Pitts attorney Robert Offer told ABC News.
The Hollywood power couple tied the knot in August 2014 in France at a ceremony featuring their children: Maddox, Pax, Zahara, Shiloh and twins Vivienne and Knox.
Pitt, 52, and Jolie Pitt, 41, started dating in the mid-2000s after meeting on the set of "Mr. and Mrs. Smith." Since then, the couple often spoke about their quiet life at home with their family.
"We wake up, we make breakfast. In our domestic life, we’re Mom and Dad," Jolie Pitt told The Wall Street Journal magazine last year. "And often we're dorky Mom and Dad, which the kids find ridiculous."
In that interview, Pitt gushed about his wife.
"When Angie has a day off, the first thing she does is get up and take the kids out. This is the most important to-do of the day. No matter how tired she might be, she plans outings for each and all," he said.
The couple starred together in last year's "By the Sea," which Jolie Pitt also directed and wrote.
This was the second marriage for Pitt, who was previously married to actress Jennifer Aniston, and the third for Jolie Pitt, who was married to Jonny Lee Miller and Billy Bob Thornton.
Carolyn Durand and Alyssa Pone contributed to this report.