But a nine-member panel still selected her for Sochi, based on past performances.
Gracie Gold earned her Olympic ticket after capturing her first national title while 15-year-old sensation Polina Edmunds took second, locking up two of the three spots.
Mirai Nagasu, who was fourth at the 2010 Vancouver Olympics, placed third and had looked set to grab the final position only to see it awarded to Wagner.
“I’m disappointed in the decision,” said Nagasu in a statement. “Though I may not agree with it, I have to respect the decision the federation made.
“And I’m grateful to everyone who has supported me and look forward to what comes next in my skating career.”
While the U.S. Olympic squad is selected largely on the results of the national championships, a nine-member selection panel has the final say and has the power to consider past results and other factors in making a decision.
The nominations still must be approved by the United States Olympic Committee before becoming official.
“I’m at a loss for words right now,” said Wagner on Sunday after learning she had made the team. “It’s been a really rough four years and I’ve been working really hard.
“It wasn’t my night last night but I’m so extremely pleased.
“I’m happy that my federation was able to see beyond one bad skate, and I can’t believe that I’m going to be able to represent the United States in Sochi.”
The other nominations were more straight-forward.
Ice dance world champions and Vancouver Olympic silver medallists Meryl Davis and Charlie White claimed their sixth U.S. title and head to Russia as the United States’ best chance for a figure skating gold.
They will be joined in Sochi by two-time reigning U.S. silver medalists Madison Chock and Evan Bates and the brother/sister partnership of Maia and Alex Shibutani.
“This is a dream come true for us,” said White. “Obviously we’re going into these Games with very high expectations.
“We’ve had a lot of great momentum over the last four years since the 2010 Olympics and we think we’ve put ourselves in a great position to bring home a gold medal.”
The pairs competition will be represented by two-time reigning U.S. champions Marissa Castelli and Simon Shnapir, and Felicia Zhang and Nathan Bartholomay.
With defending Olympic champion Evan Lysacek unable to defend his men’s title, American gold medal hopes will rest with Jeremy Abbott, who won his fourth U.S. title on Sunday, and runner-up Jason Brown.
Jeremy Abbott; Jason Brown
Gracie Gold; Polina Edmunds; Ashley Wagner
Marissa Castelli/Simon Shnapir; Felicia Zhang/Nathan Bartholomay
Meryl Davis/Charlie White; Maia Shibutani/Alex Shibutani; Madison Chock/Evan Bates
(Reporting by Steve Keating in Toronto, editing by Gene Cherry)