The couple's eldest children, Violet, six, and Seraphina, three, were attending the martial arts training in Santa Monica, Ca. and RadarOnline.com has photos.
It wasn't a regular class for Violet who walked in with a white belt and came out with an orange one, proudly clutching a certificate in her hand.
The married A-listers and their kids looked like the picture perfect family, however there was one person missing from their brood - their baby boy, Samuel.
Earlier in the day however Garner, 40, was spotted carrying him on a coffee run with Seraphina.
Affleck, 40 - who is currently starring in Argo - opened up about his daughters' hobby to talk show host Jimmy Kimmel.
"My daughters do karate," he said. "I wouldn't call it a sport as much as I'd call it discipline.
"They know that it's a way of peace and it's purely defensive and they would never use their powers to hurt others. But if you tangle with them...they'll rip your nuts off."
Ben Affleck And Jennifer Garner Take Their Daughters Out On The Town