Nadal beat the world number four 6-2, 6-1 to bring up his first win over a top-five player in more than a year and extend a hot streak after he also reached last week's China Open final.
Spain's Nadal was on court for just 64 minutes against Wawrinka, who admitted he was feeling the effects of his marathon three-setter against Marin Cilic late the previous night.
The French Open champion from Switzerland, who won last week in Tokyo, made 34 unforced errors and was on target with just 45 percent of his first serves as he folded meekly.
"For sure physically I feel the effect of last night, but also the past 10
days," Wawrinka said.
"I've been playing a lot, winning Tokyo," the Lausanne native said.
"Today, I was just struggling a little bit," he said.
"It's that simple: against Nadal you cannot do anything if you're not 100 percent."
Nadal will play Jo-Wilfried Tsonga in the last four as he bids to keep up his record of winning at least one Masters title every season since 2005.
More importantly, hours of extra work on the practice court look to be paying off as after a tough year, Nadal looks to recapture the form that brought him 14 Grand Slam titles.
"Being in the semifinals is a great result for me," the Spaniard said.
"I didn't play any semi-finals on hard court this year, now I am playing (them) two weeks in a row," he said.
"That's a big improvement for me," Nadal said.
"In terms of confidence, in terms of the level of tennis, I am playing better."
Earlier Tsonga laboured to a three-set win over big-serving South African Kevin Anderson, 7-6 (8/6), 5-7, 6-4.