The former US Open champion beat her 19-year-old opponent 3-6 7-5 6-2 in Osaka to clinch the hard court title, with her second of the year ensuring she has won more than once in a season for the first time.
The Australian wore down Bouchard with some booming forehands into an open court after pushing the Canadian out wide with a clever kick serve.
It was a fifth career title for the world number 20 and second in Osaka following a 2009 success.
The fifth seeded Bouchard began her first WTA final confidently, breaking her 29-year-old opponent three times en route to taking the set 6-2.
The second set looked to be heading for a tiebreak at 5-5 but third seed Stosur stepped up her game, breaking the Canadian as she won seven of the next eight points to seal it 7-5.
Bouchard held serve to open the deciding set but Stosur again went on a run, claiming the next four games to open up a lead she would not relinquish to seal victory in two hours and 13 minutes.
"Eugenie was playing really well today. I just had to stick it out in the second set, and I'm pretty happy with how things went in the third," Stosur said in an on court interview.
"I love playing here. I love the site and the fans are great - I always feel like I have lots and lots of support when I come to Osaka."
- Sports & Recreation