The local favorite set the tone in the first game by breaking Wawrinka with a vicious flick to land the ball on the sideline.
Nadal, who won in Madrid in 2005 and 2010, roared out to a 4-0 lead in 20 minutes.
World No. 15 Wawrinka settled down in the second set and was able to take Nadal’s service game to deuce, but Nadal returned two line-drive shots by Wawrinka at the net, before he fired the third try long. Nadal then drove in an ace to end Wawrinka’s challenge.
“Nadal showed again that he is the best on clay,” said Wawrinka, who also congratulated Nadal’s coaching staff for helping him back from his layoff. “Since he has come back he has shown that it is really tough to beat him.”