It was Sharapova's first title in Zurich, after she finished as runner-up to Alicia Molik in 2004.
The victory, achieved with the loss of just one set all week, added to the Indian Wells, San Diego and U.S. titles she earned earlier this year.
Although the second-seeded Russian will remain at number three in the rankings next week behind Amelie Mauresmo and Justine Henin-Hardenne, the win boosted her chances of ending the season as world number one.
Despite her defeat, Hantuchova's ranking will improve next week from 22 to an expected 16.
Sharapova was far more aggressive than Hantuchova in the opening set, especially with her returns, and she pressured the Slovak from the start.
Hantuchova had to hold off three break points in the first game and then dropped her serve to love, hitting consecutive double-faults, to fall behind 2-1.
Sharapova continued to dominate, breaking Hantuchova to love a second time while winning 15 of 16 points to establish a 4-1 lead. The Russian broke for a third time to take the set when Hantuchova netted a forehand.
UNFORCED ERRORS
After calling her mother to court as her coach, allowed under rules being tried out in Zurich, Hantuchova was far more positive in the second set, breaking Sharapova for 1-0.
Sharapova's efforts were more muted in the second set. She made considerably more unforced errors and failed to win a break point to level at 4-4 when she netted a tired forehand.
Hantuchova fought off five break points at 5-4 to take the match to a deciding set.
"It was weird having a little letdown in the second set, at the beginning," Sharapova told reporters. "I had opportunities to break her again but I couldn't really take them and in the last game to win the second set she served pretty well on the big points.
"But, saying that, I gave it to her in the first game. I felt like I had the chances but wasn't converting them, and finally in the third set I did."
Sharapova once more showed some of the aggression that had served her well in the first set and although she failed to take advantage of two break points at 1-0 she broke to lead 3-1 when Hantuchova netted a forehand.
That was enough to decide the match, which Sharapova closed out with consecutive aces.
"In the first set I think I was trying a little bit too much," said Hantuchova. "It was my first final for a while and I was maybe a little too excited and after the first set I tried to calm down and think more about what I had to do to come back to the match.
"I thought it was a very good match. I felt like I had my chances but I have to give Maria credit for the way she closed the match out, especially in the last game. She served very, very well. I tried to hang in there and do whatever it took to still come back, but she was putting a lot of pressure on me."
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