Olympic champion Murray, playing his first event since winning his maiden grand slam title at last month's US Open, survived a scare from the Swiss in brilliant Tokyo sunshine.
Briton Murray faces sixth seed Milos Raonic on Saturday after the big-serving Canadian squeaked by third seed Janko Tipsarevic 6-7 6-2 7-6 in an epic struggle.
The first set was all Murray, who sealed a double break after picking up a drop volley and whipping a superb lob into the corner with Wawrinka's nose still poking over the net.
Seventh seed Wawrinka had clearly not read the script and fought back to take the second, Murray smashing his racquet on the court in disgust.
Normal service resumed in the decider, Murray a touch fortunate to break for 3-1 when a forehand return clipped the net and rolled onto Wawrinka's side of the court.
A frustrated Wawrinka responded by mangling his own racquet in the next game to even up the code violation warnings from the chair umpire.
"It was a difficult match," top seed Murray said in a courtside interview after extending his winning streak to 10 matches.
"I managed to get the break in the third but there are no easy games against Stan.
"We've had lots of tough matches," added the Scot, who had won seven of his previous 11 meetings against the 2008 Beijing Olympic doubles champion. "It was the same again today."
Murray overpowered Raonic 6-4 6-4 6-2 in the fourth round of last month's US Open but the Canadian has been in red-hot form in Tokyo.
Making a bold fashion statement in a pair of blazing orange goggles, Serbian Tipsarevic had a match point in the final set tiebreak rudely snatched away by a huge Raonic serve.
Raonic, who ripped 24 aces in total, took the breaker 9-7, fittingly with another sizzling serve out wide which clipped the line, ending an absorbing match after two hours, 43 minutes.
"I played pretty well," Raonic said of his thrashing by world number three Murray in New York. "He was just too good. I just hope he doesn't play that well again."
Raonic, who also beat Tipsarevic in the Chennai final earlier this year, has been taking in ancient Tokyo from the back of a rickshaw in between matches.
"I got my samurai experience," said the 21-year-old, whose uncle is the former vice president of Montenegro. "I got to hold a sword, which was something that was really fun."
In the other side of the draw, second seed Tomas Berdych was dumped out by Kei Nishikori of Japan in a straight sets, 7-5 6-4, defeat.
Meanwhile, Marcos Baghdatis secured his place in the semi-finals with a 6-2 6-4 victory over Dmitry Tursunov of Russia.
- Milos Raonic