The famous family were dressed in pastels for church on Easter Sunday (April 16).
The pair filed the docs together and they are both seeking joint legal and physical custody of their three children.
The date of separation, as well as the division of property and any spousal support, is still to be determined. There is no prenup, which means all earnings during the marriage can be split in half, unless they agree otherwise.
The divorce news is somewhat surprising. In March, sources said Ben and Jen were calling off their divorce.
The A-listers announced their separation back in June 2015.
“Jen has called off the divorce,” a source close to Garner said last month. “She really wants to work things out with Ben. They are giving things another try.”
“There is always a chance of reconciliation,” added the insider. “They love each other. They also really, really love their kids, and those kids love their parents.”
The Accountant star recently announced his stint in rehab.
“I have completed treatment for alcohol addiction; something I’ve dealt with in the past and will continue to confront,” the Gone Girl actor shared via Facebook.
He added: “I want to live life to the fullest and be the best father I can be. I want my kids to know there is no shame in getting help when you need it, and to be a source of strength for anyone out there who needs help but is afraid to take the first step. I’m lucky to have the love of my family and friends, including my co-parent, Jen, who has supported me and cared for our kids as I’ve done the work I set out to do. This was the first of many steps being taken towards a positive recovery.”