The 19th-ranked Kudermetova overwhelmed the American 7-5, 6-1 in an hour and 24 minutes.
"I knew it would be a tough final... I need to fight for every ball and today it worked really well," said the 26-year-old.
"I'm really happy that I managed to win my second title."
She beat Pegula in three sets on the clay in Madrid this year.
Kudermetova had a tough semi-final, needing three hours and 25 minutes to defeat Anastasia Pavlyuchenkova.
She stunned four-time Grand Slam champion Iga Swiatek in the quarters.
Pegula was aiming for her second title of the season following victory last month in Montreal.
The 29-year-old went into the US Open dreaming of a first ever Grand Slam title, but her campaign came to an abrupt halt as compatriot and close friend Madison Keys recorded a dominant win in just 61 minutes.
