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The win brought the Spaniard's match record at Roland Garros to a remarkable 57-1 as he seeks to become the first player in history to win the same Grand Slam title eight times.
But to get to Sunday's final, he will have to defeat top seed and great rival Novak Djokovic, who won their last encounter on clay in Monte Carlo in April.
Djokovic had a slightly harder time of it against German veteran Tommy Haas, advancing on a 6-3, 7-6 (7/5) 7-5 scoreline.
"I think today I played my best match of this year at the tournament. I was very happy with the conditions on a court that is so emotional for me," said Nadal
"Stan was a little bit tired after his incredible match against Richard (Gasquet) which I thought was the best match of the tournament so far."
The odds were firmly stacked against Wawrinka going into what was his first French Open quarter-final match in nine campaigns at Roland Garros.
He had lost all nine previous matchups against Nadal, failing to win a single set, and had needed treatement for a leg strain during his five-set marathon win over Gasquet in the fourth round when he came back from two sets down.
The odds looked spot on in the first set as Nadal broke the Swiss player's serve in the opening game and then again in the fifth to take the first set 6-2.
Nadal then jumped out into a 3-1 lead with another break early in the second set before Wawrinka had a glimmer of hope with a break back to get to 3-3.
But that was as far as it got for the ninth seed as Nadal simply added extra muscle to his pounding groundstrokes, leaving Wawrinka reeling under their weight and precision.
Nadal ran off three quick games in a row to take a two sets to love lead and it was clear that Wawrinka's chances of another major comeback were next to impossible.
To make matters even worse, Wawrinka needed further treatment to his strained thigh even before the third set could get underway.
He did have a break point to savour as the third set got underway, but a thumping Nadal first serve erased that and then Wawrinka was broken again in the next game.
Nadal was now in full flow and Wawrinka's shoulders started to slump as he stumbled on towards inevitable defeat.
A disappointed centre court crowd tried to instill some belief into the Swiss player, but he was beyond help as Nadal ran off the four games he needed to book his place in the semi-finals.
French Open quarter-final results (x denotes seeded player):
Men:
Quarter-finals:
Novak Djokovic (SRB x1) bt Tommy Haas (GER x12) 6-3, 7-6 (7/5), 7-5
Rafael Nadal (ESP x3) bt Stanislas Wawrinka (SUI x9) 6-2, 6-3, 6-1
Women:
Quarter-finals:
Victoria Azarenka (BLR x3) bt Maria Kirilenko (RUS x12) 7-6 (7/3), 6-2
Maria Sharapova (RUS x2) bt Jelena Jankovic (SRBx18) 0-6, 6-4, 6-3
