Nadal spent only 51 minutes on court against fellow Spaniard Carreno Busta before an abdominal injury forced the world No. 21 to call it quits.
The sixth seed is fast becoming one of the best players on the ATP Tour, but he was superb in surging to a 7-6 6-3 6-0 victory over the former world number one.
"The last couple of tournaments I have had some great match matches and it is unfortunate to finish Roland Garros the way I have done", he told the press after his defeat. I still made the game and broke him in the first service game and again broke him in his first service game in the third set. "We'll see. Obviously it's not an easy decision to make, but I will see how I feel after Roland Garros and then decide what to do next".
They kissed each other on the cheeks in traditional French fashion at the end of the match after Cornet failed to return a powerful crosscourt forehand, triggering scenes of joy in the Court Philippe Chatrier stands after a 90-minute tussle.
Neither Nadal nor Thiem have dropped a set in reaching the last four, with the Spaniard losing just 22 games through five matches.
Carreno Busta was making his first quarter-final appearance at a Grand Slam.
"So far I have always played way worse match the following day if I beat a top guy".
"It's a big challenge but I am up for it", said Djokovic.
Djokovic dropped serve at the start of the second set and the expected backlash never materialised as Thiem marched towards the last four with unexpected ease.
He said: "When have you seen Djokovic lose 0-6 in a Grand Slam quarter-final?"
Djokovic will be hoping Andre Agassi can help him to come out all guns blazing when he goes into battle at Wimbledon.
Fourth seed Nadal recorded his 100th best-of-five-sets victory on clay - from just 102 matches.
"Today was a flawless match for me, I thought I played very well from the beginning", Wawrinka told a news conference. Thiem is 2-4 in his career against Nadal, 0-1 against him at the French Open.
"I don't know how many games I lost this year, but I really don't care about this".
On his status as tournament favourite, Nadal added: "I'd like to thank all those who say that I'm a favourite, but I'm on the court".
Wawrinka is now eager to gain revenge on Andy Murray after setting up a re-match of last year's semi-final.