The fourth-seeded Wawrinka missed wildly on his groundstrokes throughout the match, finishing with 34 unforced errors.
He was coming off a tough three-set victory over Marin Cilic in the quarterfinals that finished close to midnight the night before.
Nadal hadn't won against a top-five player since last year's French Open final when he defeated No. 2 Novak Djokovic for his 14th Grand Slam title.
Nadal will play Jo-Wilfried Tsonga in the semifinals on Saturday after the French player topped Kevin Anderson of South Africa 7-6 (6), 5-7, 6-4.