The 25-year-old Slovak finished sixth in the last slalom of the season at the World Cup finals in Lenzerheide, Switzerland, but it was enough to mathematically win the overall classification ahead of Lara Gut-Behrami, who didn't race on Saturday.
It was a different story in the slalom race. Vlhova failed to defend her title from last season as the best slalom skier despite leading the standings before the competition in Lenzerheide.
She was overtaken by Cortina 2021 world champion Katharina Liensberger who was the fastest in both runs, finishing 1.24 seconds in front of Mikaela Shiffrin. The Austrian is the first woman from her country to win the discipline's crystal globe since Marlies Schild in 2010/11.
Liensberger topped the final slalom rankings with 690 points, ahead of Shiffrin (655) and Vlhova (652).
"This globe means so much to me because I did everything that I could," the 21-year-old told FIS after clinching her second back-to-back World Cup race.
"I knew from last season that I was getting better, I always wanted to get better and I did everything for that."
Vlhova: "I still can't believe it!"
Ahead of Sunday's giant slalom, Vlhova leads the World Cup overall standings with 1,392 points, making it impossible for second-placed Gut-Behrami (1,256) to overtake her.
Slovakia is the 15th country to win the overall Crystal Globe on the men's or women's side.
"I can’t even wrap my head around it at the moment, as I’m still a bit disappointed after the slalom," Vlhova, who achieved six wins and 10 podiums this season, told Slovak public broadcaster RTVS.
"On the other hand, we have the big globe and that’s really hard work, because I competed in the whole program except for the downhill at the World Championship. Fighting for the overall title is extremely difficult, I can’t even describe it. I had some ideas on how hard it would be, but the reality is even harder.
"It was our goal from the beginning of the season, we went for it and I’m really happy. I will probably only fully grasp it tomorrow, when I hold the globe in my hand" - Petra Vlhova
"I’m really sorry about today, because I was leading the slalom race all season long and then I make this not great result in the last race of the season. I have to get a good night’s sleep so tomorrow’s better. Tomorrow, probably for the first time in my life, I will race without pressure, so I will try to enjoy it and race patiently while giving it all, like I always do."