Toronto, Canada – Cohen won silver at the Turin Olympics and had not skated competitively since finishing third at the 2006 world championships but her eagerly awaited comeback ended in disappointment.
The charismatic 25-year-old's error-strewn free skate left her down in fourth place and all but out of contention for one of the two spots on the American squad.
After a polished short program put Cohen in second place on Thursday, her dream of competing in a third Olympics seemed a reality but her three years on the sidelines were all too evident on Saturday.
Cohen double-footed several jumps and took a tumble as the short trip north of the border was suddenly barred.
"It was just really special for me to take this challenge this year, and train rally hard and get back into great shape, to be here, with so many people I've know my whole life," Cohen told reporters immediately following her skate.
"It was so special to come back and skate again. There wasn't sadness and wasn't regrets. I'm just really proud to be here, really proud to skate again."
Instead it will be Flatt carrying U.S. medal hopes in the women's event in Vancouver, the 17-year-old turning in a dazzling free skate to jump from third after the short program to the top of the podium with a mark of 200.11.
"It is stressful I have to admit it," Flatt said. "But I handled it very well, it was great feeling, I had so much fun.
"I'm still shaking."
A nine-member selection committee will decide who accompanies Flatt to Vancouver.
Sixteen-year-old Mirai Nagasu, who had led after the short, has a grip on the coveted spot after taking second behind Flatt but the committee could opt for third place finisher Ashley Wagner.
Injuries have kept America's top dance pairs apart for much of the last two seasons, but the U.S. nationals provided the perfect stage as their intense rivalry brought out the best in two couples expected to contend for the gold medal in Canada.
(Writing by Steve Keating in Vancouver; Editing by John O'Brien)