The former television journalist and Kennedy family heir cited irreconcilable differences but offered no additional details about the breakup.
She also did not list a date when the couple separated, although they announced they had done so on May 9.
A week later, the former action star and former governor admitted he fathered a child with a member of his household staff years ago.
Shriver's filing does not indicate the couple has a prenuptial agreement, which likely means Schwarzenegger's earnings from his career as a Hollywood megastar will be evenly divided with his estranged wife.
The couple were married in 1986 and have four children together, including two sons who are still minors. Shriver's petition seeks joint custody of the couple's sons, ages, 17 and 13.
Schwarzenegger's spokesman Adam Mendelsohn declined comment in an email. Shriver's attorney Laura Wasser did not immediately return a phone message seeking comment.
Shriver stood by her husband's side as he ran for California's governorship in 2003 even after the Los Angeles Times reported accusations by several women that they had been groped by the movie star.
Schwarzenegger later said he "behaved badly sometimes" and was twice elected to the governorship.
He failed to fix the state's chronic budget problems and left office in January with an eye toward environmental projects and a return to the big screen.
One of his projects was an animated collaboration with comic book legend Stan Lee titled "The Governator," but the project was shelved after Schwarzenegger admitted fathering the child out of wedlock.
Shriver placed her journalism career on hold while her husband served as governor, and her future has been more uncertain. She has appeared in videos posted on YouTube in which she talks about stress in her life, the weight of expectations and the search for faith in a troubled world.
The filing was first reported by celebrity website TMZ.