Stewart’s single down the third base line scored the runner from third as the defending champions rallied with three runs in the tenth off Japan starter Yukiko Ueno.
The tournament doubles as a qualifier for the 2020 Tokyo Olympics.
The U.S. secured its spot in the Olympics earlier Sunday when Japan beat Canada 3-0.
Softball and baseball were dropped from the Olympic program after the 2008 Beijing Games but have been restored for 2020.
Sunday’s final was a re-match of the gold medal game at the 2008 Beijing Olympics that Japan won by a score of 3-1.
Ueno also went the distance in the win over Canada, striking out seven while giving up four hits and no walks.
By JIM ARMSTRONG , Associated Press