ET confirms that Pechenik submitted the paperwork at the Los Angeles Superior Court on Tuesday. The actress and film producer share two children together, daughter Elsie Otter Pechenik, 4, and son, Charlie Wolf Pechenik, 2.
The filing comes a month after the pair announced that they were separating after four years of marriage.
"After much discussion and a long period of contemplation we have decided we are better off as friends, business partners and co-parents rather than life partners," the joint statement to ET read. "We remain committed to our business, our values, and most of all, our children. Thank you for respecting our privacy at this time."
Deschanel and Pechenik got married in June 2015 in an intimate ceremony, after less than a year of dating. They announced that they were expecting their first child together in January of that year, and their engagement shortly thereafter.
Zooey is currently dating Property Brother Jonathan Scott and made their relationship Instagram official this week.
A source confirmed Deschanel and Scott's romance to ET last month, revealing their relationship was "still new." The pair met while filming Apple TV's Carpool Karaoke series with their siblings and "started out as friends but then realized they liked each other."
At the time, ET's source said that the new pair had only been on a few dates, but were having a lot of fun together.