Vondrousova, Wimbledon champion in 2023, had impressed in New York with upset victories over seventh seed Jasmine Paolini and ninth seed Elena Rybakina.
But injury again derailed the 26-year-old, who has endured long spells on the sidelines in recent seasons. She was one of three Czech women to reach the quarter-finals at Flushing Meadows.
Top seed Sabalenka will now face American Jessica Pegula in the semi-finals in a rematch of last year's final.