The Belgian world number one needed just one hour and 22 minutes to take the comprehensive win and move above Venus Williams to second in the list of active grand slam winners.
She also becomes the first woman to ever to beat both Venus and Serena Williams en route to winning a grand slam crown and the first to win the tournament without dropping a set since Serena did it in 2002.
"It's such a great feeling," Henin said after the match, which was a replay of the 2006 French Open final won by the Belgian. "I had two amazing weeks and played my best tennis."
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Henin, who won the title in 2003, broke the fourth seeded Russian in the very first game of the match and was never threatened after that.
Thanks to some play from the baseline the 25-year-old Belgian broke again in the third game and it wasn't until the fifth that Kuznetsova finally won a game by holding serve.
After blazing through a love-service game in the sixth, Henin completed the 6-1 opening set in just 33 minutes breaking the 2004 champion for a third time as Kuznetsova fired a backhand error into the net - one of 29 unforced errors for the 22-year-old Russian.
The second set started slightly better for Kuznetsova, who pressed the diminutive Beglian a bit more in Henin's first service game and then took her own opening service game to love.
But then at 2-1 in the second, Henin struck again as the error-prone Kuznetsova was made to save three break points before surrendering the critical break of serve on the Belgian's fourth chance.
Kuznetsova missed a golden opportunity to break back in the next game hitting repeated errors on back-to-back break points, and then watching as Henin fired home a nervy ace and a big overhead smash at the net to hold serve.
The two woman held comfortably in the next three games, setting up a dramatic ninth game.
Serving for the set at 5-3 Henin opened up with an ace, but then hit back-to-back double faults after a highly audible jeer was heard from the crowd in between serves.
Kuznetsova then pressed Henin, who lost last year's final at Flushing Meadows to another Russian Maria Sharapova, to a double break point.
The Belgian saved the first with an emphatic ace and then outlasted Kuznetsova in the second after a long baseline rally bullying the Russian into an error.
Another double fault handed Kuznetsova, who will be the new world number two when Monday's WTA rankings are released, yet another chance to break.
But when the fourth seed failed this time with a horribly mis-hit forehand, the conclusion seemed set in stone.
Henin pressed Kuznetsova into yet another error to get to championship point and then made the gutsy decision to serve-and-volley before beating the Russian with another drop-volley at the net to earn her second grand slam title of the year on top of her French Open win in June.
"She played an unbelievable tournament and an unbelievable game today," Kuznetsova said.
"I hope to be back with better game in the final next time."
Follow LIVE coverage of the men's final between Novak Djokovic and Roger Federer from 21:30 BST on Sunday on eurosport.yahoo.com.
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