Since his return from seven months on the sidelines with injury Nadal has played seven tournaments, winning five and reaching the final of the other two.
The world number five needed just 71 minutes to cruise past Wawrinka, who was never really in the match despite producing a more competitive second set.
The Swiss number two, who will move up to number 10 in the world when the new rankings are released on Monday, has now lost 18 out of the 18 sets he has played against the Spaniard, losing all nine of their matches since they first met at the Australian Open back in 2007.
Nadal, on the other hand, will head into the Rome Masters next week and the French Open at the end of the month with renewed vigour, having bounced back in style from his confidence-sapping defeat to world number one Novak Djokovic in the Monte Carlo Masters final two weeks ago.
The victory in Madrid was Nadal’s 55th career title, 40th on clay and 23rd in the Masters series, with the Rome Masters and the French Open offering yet more chances to extend those record numbers before the tour switches to grass in June.
"Maybe this win is even more special given where I have come back from," Nadal said in an interview with Spanish television broadcaster La Sexta.
"Playing in Madrid is always very exciting for me and the tournament couldn't have worked out better," he added.
The world number five opened the match in brutal fashion, breaking in the opening game. The Spaniard actually needed three attempts to secure the opening break, missing what for him would normally be regulation forehands. But he quickly made amends, finding the whipped forehand winner down the line to bring up a third break point before a forehand passing shot winner across court brought him the first game.
A second break followed shortly after in the third game before Wawrinka finally got on the scoreboard in the fifth, avoiding the ignominy of a dreaded bagel set.
But it was only a temporary respite for the Swiss as Nadal served out the set three games later, having not dropped a single point behind his first serve.
The second set was a more tightly fought affair as Nadal was made to wait until the seventh game before he secured a break, the Spaniard having not been able to take advantage of break points in the fifth.
In the end though it was a poor game from Wawrinka that caused the damage, the Swiss conceding his serve on a double fault after a sloppy forehand error had given Nadal the break opportunity.
Wawrinka did well to hold for the loss of just the one point when serving to stay in the match, but with the Swiss having been unable to earn himself a break point all match - and only once having even pushed Nadal to deuce - it was only a matter of time until the Spaniard sealed victory.
As the clock ticked over to one hour and 11 minutes, Wawrinka pushed a backhand long and Nadal fell to the ground in his customary celebration of a tournament win.