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Badosa posted on social media that the injury has forced her to shut down her season.
Ninth seed Kviotova brushed aside the challenge of Belarusian Aliaksandra Sasnovich.
Swiatek reached her first Indian Wells final after overpowering former champion Simona Halep 7-6(6), 6-4.
In their first career meeting, Muguruza's superior firepower put Badosa on the back foot from the outset.
Karolina Pliskova missed the cut despite her comeback victory over Barbora Krejcikova.
Sabalenka fought back from a set down to beat Swiatek 2-6, 6-2, 7-5 in another match.
Badosa becomes the first Spanish woman to win the tournament in the California desert.