The 20-year-old had been the 17th seed in the year's final Grand Slam event that begins on Monday.
Vondrousova won her only WTA title at Biel Bienne, Switzerland in 2017.
She has lost finals at Budapest and Istanbul this year as well as at Roland Garros to Australia's Ashleigh Barty, the US Open's second seed.
China's Zhang Shuai, who was the next eligible player to be seeded, will move to Vondrousova's spot in the draw and Zhang's spot will be taken by a qualifier or lucky loser.
Zhang is now in the same eighth of the draw as Czech third seed Karolina Pliskova and will face Swiss Viktorjia Golubic in the first round, leaving a qualifier or lucky loser to open against Germany's Laura Siegemund.