The actor wrote on his Twitter page about the babies, who were born on Tuesday.
He tweeted: "Babies!! On 10/12, Gideon Scott and Harper Grace entered the Burtka-Harris fold. All of us are happy, healthy, tired, and a little pukey."
Burtka has made several cameo appearances in Harris's sitcom How I Met Your Mother, while Harris will be directing movie comedy Aaron and Sarah in the New Year.