The 'New Girl' actress lodged the papers in Los Angeles Superior County Court on December 27, citing "irreconcilable differences" as her reason for splitting from the Death Cab For Cutie frontman.
The papers, which were obtained by TMZ.com, state the couple - who were married for two years - officially separated on October 31, 2011.
Following their break-up, Zooey refused to discuss the cause of the break-up but insisted everything was amicable.
She said: "We're friendly. It's all fine."
Just months before the announcement, the '(500) Days of Summer' star said she enjoyed being married.
She said: "You can't expect to make no effort. You still have to make the effort and be kind and understanding. It sort of just solidifies your commitment."
Ben - who also fronts the band She and Him with Zooey - said in September he thought of his wife as "very beautiful".
He revealed: "I'd seen her movies and obviously I thought she was very beautiful. [When we were introduced] I was awestruck that she was even talking to me!"