The 34-year-old royal approached his father after Meghan's father, Thomas Markle, pulled out due to health issues.
In a new BBC documentary, Prince, Son and Heir: Charles at 70, Harry says: “I asked him to and I think he knew it was coming and he immediately said, ‘Yes, of course, I’ll do whatever Megan needs and I’m here to support you.’ “
“For him that’s a fantastic opportunity to step up and be that support, and you know he’s our father so of course he’s gonna be there for us.”
During the ceremony, as Charles led Meghan down the aisle at St George's Chapel, the prince was seen whispering, "Thank you, Pa."
Camilla, Duchess of Cornwall, admitted she couldn't see the exchange between father and son at the altar but later watched it back on TV.
“I think that was very touching, sitting where I was, you couldn’t hear what he said. But afterwards watching it on the television, I think it was a very…it was a lovely gesture,” she says.
Of the emotional moment, Harry adds: “You’ve gotta say thank you. Just because he’s my father that doesn’t mean I can just sort of go, ‘Okay, that’s all, I’ll take it from here'.”
Harry then adds, “No, that is what I wanted to say but…and I was very grateful for him to be able to do that.”
Camilla then spoke fondly of the moment that later went viral - Prince Charles holding Doria's hand as they walked into the private room to sign the registry.
“A lot of people, seeing my husband actually take the bride’s mother by the hand to sign the registry, it’s something that moved everybody.
“It’s the things he does behind the scenes that people don’t know about. I don’t think people realise quite how kind he is.”