World number one Nadal was pushed to the limit by Wawrinka in a highly competitive first set, but the relentless Spaniard came out on top in a gripping tie-break lasting more than 20 minutes.
It was one-way traffic in the second set as he prevailed 7-6 (12/10), 6-1.
Top seed Djokovic kept his side of the bargain under floodlights at the Qizhong Tennis Center, withstanding a feisty challenge from Frenchman Gael Monfils to win his quarter-final 6-7 (4/7), 6-2, 6-4.
Nadal, who has won 10 titles -- including the French Open and US Open -- this year, fended off three set points for Wawrinka, against whom he now boasts an 11-0 record, before taking his fourth opportunity to win the opener.
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A dispirited Wawrinka ran out of steam in the second set against never-say-die Nadal, who regained the number one ranking this week and is chasing a record sixth Masters title in a single season.
But Monfils, cutting an imposing figure in his bright orange top with a shock of dark hair, let his intensity slip at the start of the set and Djokovic immediately seized the initiative with a break.
A time violation against Monfils rattled the Frenchman, who became embroiled in an argument with the umpire and was soon flat on his back receiving treatment on his abdominal muscles as the set slipped away from him.