Last week the audience of US comedy show, Saturday Night Live, laughed when Elton said that this was the case, thinking he was joking.
In his opening monologue, the 64-year-old singer said: "For those of you concerned that we are unusual parents, don't worry, it's not like we are the only two people involved in the child's life.
"His godmother is Lady Gaga... which is ironic, because I've always said that Mars ain't the kind of place to raise your kids. And Gaga loves Mars. She says Mars has good schools and great discos."
Now David Furnish has spoken out, confirming the identity of Zachary's godmother calling quirky singer Lady Gaga "inclusive" and "tolerant".
Elton's husband added: "She believes that you can be whoever you want to be and that we don't have to live in a world of conformity... That's the best message in the world. The freedom to be who you are, do what you want and love who you want to love."