The actor posted the video to Facebook, saying: "I want to say Happy Mother's Day to all the mums in my life - my mum, Chris, and my amazing wife, Jennifer, who is an incredible, spectacular, world-class mum, and I want to thank her."
Affleck also called on viewers to share the video with "the Mothers and Grandmothers in your lives in honour of their sacrifices, selflessness and courage".
The video was shot during the star's recent trip to the Democratic Republic of Congo, and features imagery of Congolese mothers and children.
Affleck founded the Eastern Congo Initiative in 2009, an organisation which helps Congolese residents develop sustainable approaches to infrastructure.
The 39-year-old, who rose to fame with his movie Good Will Hunting, has recently become more involved in activism. In March, he lent his support to the controversial Kony 2012 campaign.
He recently wrapped filming on Argo, an Iranian hostage drama.
His next project will be Runner, Runner, in which he will star alongside Justin Timberlake.
Watch Ben Affleck's Mother's Day message below: