The Springboks thrashed favourites England 32-12 in Yokohama on Saturday and tennis superstar Federer sent a video message praising their achievement.
Federer's mother, Lynette, was born in South Africa and the 20-time grand slam champion clearly enjoyed the nation's success in Japan.
"Siya, it's Roger here. Couldn't be more happy for you and the team," he said in a video shared on the Springboks' Twitter account on Sunday.
"What a victory, what an amazing team effort. You guys spent so much time together and you ended up with the big win.