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It was the Spanish world number five's fifth title since he returned from a seven-month injury layoff in February and was more evidence that his troublesome knees are not about to bring his career to a premature end.
Nadal now heads to Rome, where he beat world number one Novak Djokovic in last year's final, for another Masters event on his favoured surface before the French Open starts at the end of this month.
Since he recovered from his latest knee problem, the 26-year-old has won the events at Sao Paulo, Acapulco, Indian Wells, Barcelona and now Madrid.
He also reached the final at Vina del Mar and Monte Carlo and Sunday's triumph was his third in front of his adoring home fans in the Spanish capital.
"Maybe this win is even more special given where I have come back from," Nadal, a seven-times French Open champion, said in an interview with local television broadcaster La Sexta.
"Playing in Madrid is always very exciting for me and the tournament couldn't have worked out better."
Wawrinka, who came through gruelling matches against Jo-Wilfried Tsonga and Tomas Berdych on the way to his second Masters final, never looked like claiming a first win against Nadal at the ninth attempt.
Nadal broke Wawrinka's serve three times in the match and such was his dominance, the Spaniard did not face a single break point. He collapsed on to his back in celebration when Wawrinka's backhand went long on match point.
The red dirt clinging to Nadal's shirt was a reminder that a year ago he had threatened to boycott the 2013 tournament if organisers had stuck with the controversial blue claycourt they had unveiled last year, when he was knocked out in the third round by compatriot Fernando Verdasco.
Wawrinka has never taken a set off Nadal in their nine meetings and said he had not been at his best physically or mentally on Sunday after an intense couple of weeks.
The 28-year-old arrived in Madrid having beaten Nadal's countryman David Ferrer in the final in Estoril last Sunday, his fourth career title.
"Even if I'm playing my best tennis and completely fresh, it's really, really tough to beat him (Nadal)," the Swiss told a news conference.
"If you're not completely there then he's killing you, like he did at the beginning of the match.
"It was tough for me. I didn't find the way how to play my game, how to be aggressive on the court. He was also dictating the points. Against him, it's impossible.
Nadal's 40th clay crown puts him equal second with Thomas Muster on the list of career title winners on the surface and six behind leader Guillermo Vilas.
He has the best record on clay in the professional era and has won 40 of his 46 finals. He also has the most Masters titles with 23, two ahead of Roger Federer.