Zverev admitted his French Open exertions had finally caught up with him after losing to Thiem.
Second seed Zverev had fought through three consecutive five-setters and spent almost two and a half hours longer on court than Thiem.
So it came as no surprise when the 21-year-old German, in the last eight of a grand slam for the first time, began to cramp up badly.
He suffered a muscle injury in his leg during the first set and had it heavily strapped up by the trainer during the second.
Canny Thiem, the seventh seed from Austria, consistently served wide to get his opponent stretching before working him all around the court.
Zverev needed more running repairs at the start of the third set but it was to no avail, Thiem ending his entertaining run with a comprehensive 6-4 6-2 6-1 victory.
"How close was I to pulling out? I thought about it. I definitely thought about it," said Zverev.
"But, you know, I didn't want to pull out for the first time of my career in a grand slam quarter-final.
"I knew I wasn't going to win the match. There was no way for me. I mean, I could barely move. I couldn't serve. I couldn't really do anything.
"But I still wanted to finish the match and kind of give the credit to Dominic. He deserves to be in the semi-finals. End on a loss and not on a retirement.
"I actually felt good today. Waking up in the morning, I actually felt 'OK I can play five sets again'.
"I thought it was going to be a tough, physical match, but unfortunately my body didn't hold up."
For Thiem, the seventh seed from Austria, a third consecutive Paris semi-final beckons.
"It was tough for him today, he's one of the fittest guys on tour," he said. "It's tough to play three five-setters in a row.
"I hope that we have many more encounters against each other at this stage or even later in a grand slam."
Former world number one Novak Djokovic was stunned in the quarter-finals at Roland Garros by world number 72 Marco Cecchinato, and then cast doubt over whether he will play at Wimbledon.
Italian Cecchinato won in four sets, scrambling over the line in an epic tie-break on his fourth match point.
Afterwards a dazed Djokovic, who has struggled with injury for much of the last year, was asked when he planned to make his first grass-court appearance.
He replied: "I don't know. I don't know if I'm going to play on grass. I don't know. I don't know what I'm going to do. I just came from the court. Sorry, guys, I can't give you that answer. I cannot give you any answer.
"How do I regroup? I don't know. I'm just not thinking about tennis at the moment."
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