American Williams, who is chasing a third consecutive triumph at the premier clay event in the Spanish capital, dispatched the 17-year-old Swiss, ranked 98th, to set up a meeting with unseeded Chinese Peng Shuai.
Bencic, the youngest player in the Madrid draw who is making her debut at the tournament, broke the Williams serve once in the opening set but crumbled thereafter and lost her own five times.
Maria Sharapova of Russia, the eighth seed, and 11th-seeded Serb Ana Ivanovic also went through, seeing off Czech Klara Koukalova and American Madison Keys respectively.
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- Petra Kvitova