The Spaniard, who recently took the world number one ranking from Novak Djokovic, headed into the final eight encounter favourite to progress into the semi-finals, but it was a testing start for Nadal.
Wawrinka was able to hold firm in his service games by saving three break points, leaving Nadal frustrated on the court, but the Spaniard matched his opponent until a tie-breaker was needed to separate them.
Both competitors remained tight in the set decider and it took Nadal 12 games to snatch the one-set lead in just over an hour.
Wawrinka had a mountain to climb, but losing the first set appeared to take it out of the Swiss pro, who lost his opening service game, allowing Nadal to take control of the court.
A further two break points for Nadal booked his place in the semi-finals, while Wawrinka could only get one game on the board in the second set.