Yet, United States coaches spun the surprise result as a win-win for the women's team that expects to battle China, Russia and Romania for supremacy in August's Beijing Olympics.
"The close competition is inspiring everybody to work hard and just shows that nobody has places nailed down to the ground," Martha Karolyi, coordinator of the US women's gymnastics said. "You have to improve yourself."
It was the first time that Johnson, 16, had tasted defeat since joining the seniors' ranks in an all-conquering 2007 campaign in which she won the US nationals and the world all-round title. Liukin, two years older and the winner of nine world championship medals, showed she was fully back in the frame after recovering from an ankle injury that held her back last year.
"It's going to be a tremendous competition, particularly between these two," Bela Karolyi, Martha's husband and famed coach who is chief of the US team training centre at the couple's Texas ranch, said about the Olympics.
Johnson's coach, Qiao Liang, did not see the Cup result as a setback for his gymnast, who fell during the opening rotation in an attempt to land the difficult Yurchenko vault with two-and-a-half somersaults for her first time in competition.
"I think that's a very difficult vault, only three people are doing it in the world," said Qiao, a successful Chinese gymnast who settled in Iowa more than a dozen years ago after going to college there. "We are planning to do it in Beijing.
"She made a mistake on that but I think it was a valuable one, a great learning experience.
‘Great performance’
"Other than that, it was a great performance. She not only demonstrated she is a very powerful gymnast but, as far as mental strength and her attitude, she showed she's a champion."
Qiao, who owns Chow's Gymnastics where Johnson trains, brought his pupil to the Karolyis' attention three years ago.
"I recall that I received a video from Shawn's coach, showing someone I might like to include in the training programme because someday she can make a contribution to the US team," Martha Karolyi said.
"I said: 'Why this coach is pretty confident.' And here was this little, bouncy girl. I could see some potential. I told him, next training camp she's invited. The coach was right."
Johnson, with her pixie good looks and explosive power, has sparked excitement in others close to US gymnastics.
"She's powerful, she's graceful, she's fun to watch. She's got a bubbly personality," said 1984 Olympic all-round champion Mary Lou Retton. "It is so hard to make it look easy and fun and she's got that ability. I don't know if that's a taught ability, I think you have to have it and she's got it.”
"You can be a powerful gymnast and not be top in the world. You can be a graceful gymnast and not be top in the world," Miller said. "You have to have that combination of the two.”