Nadal defeated Wawrinka, the world No. 8, 7-6 (7-5), 7-6 (8-6) in a 2-hour, 13-minute battle that was one of the tightest of the series between the two.
Nadal improved to 2-0 in Group A play and, with two straight-set wins, locked up a place in the tournament semifinals. He also closed out No. 2-ranked Novak Djokovic's chances of catching Nadal for the world No. 1 ranking this year.
Wawrinka drops to 1-1 in round-robin play and is tied with No. 6-ranked Tomas Berdych, who wrapped up Wednesday's play with a 6-4, 6-4 win over third-ranked David Ferrer. Ferrer is 0-2 in Group A with a match against Wawrinka left on his round-robin schedule.
Nadal hasn't lost in his 12 meetings against Wawrinka -- in fact, he hasn't dropped a set -- but none of the previous meetings was as close as Wednesday's match in which Nadal won 83 points and Wawrinka 80.
Nadal had break advantages in each set but Wawrinka answered both times and forced tiebreakers, which were both tied until the very late stages when Nadal managed to win back-to-back points and claim the sets.
Berdych played a very solid match against Ferrer, winning almost 80 percent of the points on serve and not allowing Ferrer a break opportunity. Berdych had plenty -- nine on the day -- and managed a break in each set.
Group B is to return to action Thursday with No. 7-ranked Roger Federer scheduled to go against ninth-ranked Richard Gasquet in the early match. Both dropped their first matches in the tournament. Djokovic is to face No. 5 Juan Martin del Potro in the late match Thursday.
The top two finishers on each group advance to the tournament semifinals.