Murray, fighting for the year-end first place in the world rankings, took 86 minutes to defeat the Swiss number one 6-4, 6-2, Xinhua news agency reported.
He also improved to 10 wins and seven defeats against Wawarinka, although winning one game was enough to send him to the last four.
The 29-year-old topped the group with a perfect record in the second group, beating Marin Cilic of Croatia in the first match and edged fifth seed Kei Nishikori of Japan in the second.
Nishikori also reached the semifinals as the second place finisher in the group, making his match against Cilic later meaningless.
Murray will fight for the final berth against fourth seed Milos Raonic of Canada and Nishikori meet Serbia’s Novak Djokvic.