Garner shared a black and white photo of Affleck on Sunday, adding a tender caption about the father of her three children.
"Our kids are lucky to have a dad who looks at them the way you look at them and loves them the way you love them, [Ben Affleck]," she wrote with hashtags, "three lucky kids," "have a great day" and "happy father's day."
Affleck posted a picture of a sign one of their children made for him that read, "I love you, Dad! You are my superhero."
"I can think of three incredible reasons why today is so special. Happy Father's Day to all the dads and father figures out there, and to the women that empower them to be the best they can be. We are all so fortunate beyond measure," the Justice League actor wrote.
Affleck and Garner have three children, Samuel, 6; Seraphina Rose Elizabeth, 9; and Violet, 12. Garner and Affleck married in 2005 and split in 2015, filing for divorce just last year.
Last week, Garner and Affleck went to Violet's elementary school graduation in Santa Monica, although they left separately, reports the Daily Mail.
In a 2016 interview with Vanity Fair, Garner said their marriage was "real" and not just something for the cameras.
"It wasn't for the cameras. And it was a huge priority for me to stay in it. And that did not work," she said.
Garner also said last fall she still has not been on a date since the split.
"I would not have chosen this life for myself or for my kids. I would not choose to be single or be in this position. It's something that we are working through. I haven't been on a date and I am not interested in dating," she told News.Com.Au. "People want to set me up and I am just like, 'No thank you!'"
"Men are last on Jen's list. First comes her children, then her career and then a man," the source said. "She is back. She has thrown herself into her work and her success... She is killing it and those [closest to her] couldn't be more proud."
Meanwhile, Affleck has started dating. Last year, he began seeing Saturday Night Live producer Lindsay Shookus. He also bought a bachelor pad in the Pacific Palisades neighborhood for nearly $20 million earlier this month.
Garner was seen in Love, Simon earlier this year and will next be seen in the action thriller Peppermint on Sept. 7. As for Affleck, he is working on Triple Frontier with Oscar Isaac and Charlie Hunnam.