Vlhova shook off a second-run challenge by Shiffrin, the overall winner of the crystal ball, to claim Saturday's race in Aspen, Colorado, by 0.24 seconds in 1:32.00.
Overall giant slalom winner Marcel Hirscher of Austria was more successful, scoring a half-second victory over Germany's Felix Neureuther in the men's race.
The 22-year-old Shiffrin stood third after the first run in softening snow, trailing Vlhova by 0.07 seconds.
The American temporarily grabbed the lead on the second run with a total time of 1:32.24 with only two skiers left.
But one of those skiers was Vlhova, who produced a strong finish to claim the victory. Sweden's Frida Hansdotter finished third in 1:32:35.
Despite the loss, Shiffrin became only the third U.S. woman to win the overall title. Her closest rival, Ilka Stuhec, withdrew from the slalom on Friday.
Hirscher needed an impressive second run to capture the giant slalom race.
The Austrian had been 0.01 of a second behind Germany's Felix Neureuther after the first run, but dominated the second.
Shiffrin became only the third U.S. woman to win the overall title. Her closest rival, Ilka Stuhec, withdrew from the slalom on Friday.
"It’s been a goal and a dream of mine since I was five years old, and it’s really difficult to understand something that finally happens after 20 years," said Shiffrin when asked about winning the first crystal globe of her career.
She finished the season with 840 points in the slalom standings with Veronika Velez Zuzulova of Slovakia second at 565 and Wendy Holdener of Switzerland third with 455.
Shiffrin also hopes to have a say in the women's giant slalom on Sunday as she chases season leader Tessa Worley of France.
Hirscher needed an impressive second run to capture his third consecutive giant slalom race.The Austrian had been 0.01 of a second behind Neureuther after the first run, but dominated the second.
His total time of one minute, 49.79 seconds easily gave him the win over Neureuther (1:50.32) France's Mathieu Faivre joined them on the podium with a total time of 1:50.98.
For the season Hirscher claimed his sixth consecutive overall World Cup title and fourth in grand slalom. Hirscher finished the giant slalom season with 733 points for a dominant victory over Faivre with France's Alexis Pinturault third.
"I’m super, super happy protecting the globe from Alexis Pinturault this season," Hirscher said.
"It means a lot to me because at the beginning of the season he was unbelievably fast, so I proved myself to be pretty good during the season."
Read the original article on Eurosport: Vlhova denies Shiffrin slalom victory at Aspen