Wagner won with 69.50 points while Japan's Mai Mihara was second on 65.75 and American Gracie Gold, the reigning US women's champion and a Chicago hometown favorite, took third with 64.87 points.
Gold led the women's world championships after the short program but a poor long program saw her fall to a fourth-place finish.
Canada's Gabrielle Daleman was fourth on 64.49 with Japan's Mao Asada, a three-time world champion and 2010 Olympic runner-up, fifth on 64.47.
In the pairs short program, Russia's Evgenia Tarasova and Vladimir Morozov, the fifth-place duo at the world championships, won with 75.24 points.
Americans Haven Denney and Brandon Frazier were second on 67.29, while Canada's Julianne Seguin and Charlie Bilodeau, who won gold at the Autumn Classic in Montreal, third on 66.49.
The Skate America women's and pairs crowns will be decided in Saturday's free skate finals.