Seeking his 18th grand slam trophy, Nadal was stunned in a first set won to love by Thiem before the Spaniard came back to take the next two.
The Spaniard had appeared the more tired of the two but he roused himself for one final effort and emerged victorious when Thiem sent a final smash long after four hours and 49 minutes.
Up next is a semi-final clash with the resurgent giant that is Juan Martin del Potro and Nadal has less than 48 hours to recover for his clash with the Argentine.
(AAP )Dominic Thiem pushed Rafael Nadal to five sets in their US Open quarter final.
Nadal was completely dismantled by Thiem in the first set as the American crowd was shocked into silence in NY, the Austrian hitting vaporising forehands and backhands to wrap up the opener in just 24 minutes - tallying 13 winners, five aces and 24 points in total compared to just seven from the former. Nadal beat del Potro last year in the semifinals at Flushing Meadows, and again this year in the semifinals of the French Open. "You are very good", Nadal said.
AFTER almost five hours on court, world No.1 Rafael Nadal and rising challenger Dominic Thiem had exhausted their tanks.
The fourth set was a wild 81-minute ride that began with Thiem facing break points, saw the Austrian threaten a double break before being pegged back and then a tired Nadal miss a chance to win the match.
The marathon tussle continued in the fifth and final set, Thiem fending off a triple break point by coming from love-40 down to make Nadal serve to stay in the championship and three-time US Open victor did before prevailing in a do-or-die tie-breaker. "Every match really means a lot to me".
"He did all the things well to win the match", Nadal said.
The defending champion has been severely tested in each of his last three matches, with Karen Khachanov and Nikoloz Basilashvili also taking a set off him, but the 32-year-old remains one of the greatest fighters in sporting history and he overcame another major hurdle. "I don't think he's really sorry", said the 25-year-old.
Perhaps Thiem, after a change of socks and shoes, looked the fresher going into the decider but he needed to save two break points at 2-2, one with an ace, to maintain parity. "He is young and has plenty of time to win tournaments".
With the mercury hitting 35C and humidity at about 50 per cent, the US Tennis Association invoked its new extreme heat policy, which allowed the players to take a 10-minute break after the third set. "Forever I'm going to remember this match, for sure", said Thiem after his first ever hard court match against Nadal.
When the ninth-seeded Thiem forced deuce in that game, Nadal rewarded his friend with a small clap from the other end of the court. "Beating John in these kind of matches is like an epic, an epic match".
Even the tiebreak was close, with Nadal edging ahead for 6-5 before the Austrian sent a ball sailing long to wrap up a long evening of brutal hitting.