She had a shaky landing at the end of her combination jump, one of seven required elements.
Thomas did the same combination jump but in reverse order - a double loop-triple toe - which is harder.
She said she had felt fine back home but failed to land her last attempt at a triple combination jump last week.
She completed the combination jump and from that point the crowd and the judges clearly were behind her.
She had a shaky landing on her triple lutz and double toe, in the first combination jump.
But she opted for the lutz and held on to complete the double-toe in her combination jump.
"A combination jump wasn't life or death," Kwan said.
Even without a combination jump, Lipinski's 14 scores showed eight 9.9's and six 9.8's.
She missed her first combination jump and hit only two of five triples.
This jump is often used in second jump of combination jump.