Cruising for most of the first set and a half against Kei Nishikori, when the roof was shut at 3-3 in the second it changed the entire complexion of the quarterfinal and the Japanese shotmaker rallied to defeat the world's most in-form tennis player 1-6 6-4 4-6 6-1 7-5 in four hours.
A sound similar to a gong that reverberated around Arthur Ashe stadium during a key point in the fourth set also unsettled world No. 2 Murray, who just last month crushed the 2014 US Open finalist en route to a historic second Olympic singles gold medal.
Murray had won 26 of his last 27 matches to close the gap in ranking points on top-ranked Novak Djokovic and was keen to earn the No. 1 position at some stage this year. His unexpected reverse is a major setback.
Nishikori, meanwhile, ended an 0-for-12 slump against top-two opposition. Not since beating Djokovic on a sweltering day in New York two years ago had he toppled a world No. 1 or No. 2.
He will face either twice grand slam winner Stan Wawrinka or 2009 tournament champion Juan Martin del Potro in the last four.
"There were many ups and downs," Nishikori, ranked seventh, told the crowd. "It was a tough start. I didn't start very well. In the end I (played) great tennis, so I'm very happy."
Nishikori opts for an attacking brand of tennis that Roger Federer, for one, enjoys watching and particularly in the final two sets he did the majority of dictating from the baseline. He picked on Murray's second serve -- Murray's percentage of points won behind the second delivery dipped to 21 in set four -- and for the most part, sparkled at the net.
Overall he struck 60 winners against one of the game's top defenders.
"I think definitely under the roof he was able to dictate more of the points, play a bit closer to the baseline than me and take the ball on a little bit more," Murray told reporters. "At times I was doing more of the running.
"In the first set and a half and when we played at the Olympics it was the other way around."
Murray took issue with the roof not being reopened when the weather improved. At Wimbledon, for example, when the roof on center court is used during a match it must stay on for that match.
At the US Open, organizers didn't have such a rule in place.
"We were told at the beginning of the event and also today that if the weather is good they will open the roof during the match," Murray said. "(If) that's the case, why it didn't happen today I don't know.
"Delays and stuff aren't good for TV and people that are watching, you want a continuous match.
"But you want to complete as many matches outdoors as possible."
Nonetheless, Murray had regained the momentum and held a second break point at 1-1 in the fourth when the loud sound went off mid-point. Chair umpire Marija Cicak ordered the point to be replayed, which irked Murray, who subsequently discussed the matter with tournament referee Wayne McKewen.
"It was the fourth time it had happened in the match and it was the first time that we stopped the point," said Murray, the 2012 US Open champion. "I was just curious as to why that was, and that was it."
Nishikori felt the point should have been replayed.
"I mean, definitely," he said. "My concentration went off." Later the tournament said a faulty digital audio sound processor was to blame and would be replaced prior to Wednesday's night session.
A rattled Murray lost seven straight games to trail 2-0 in the fifth, at which time he roared at his camp to encourage him. Still, it appeared the reigning Wimbledon titlist would escape because of Nishikori's nerves.
Murray made it 2-2, only for Nishikori to lead 4-2.
At 4-3, Nishikori dropped serve from 40-0, making a rare volley error on a comfortable volley at 40-30.
But instead of Murray surging to victory, he was broken at 5-5 when Nishikori stretched to make a stab volley. Murray slammed his racket into the net in frustration.
Nishikori began the final game with a double fault, yet didn't commit another error and for the first time in his US Open career, Murray lost a match when leading two sets to one.
He was disappointed, obviously, with the outcome but pleased with his play the past few months overall.
"I pushed myself as hard as I could over the last few months, and I'm very proud of how I have done," said Murray. "You know, if someone had offered me the summer that I have had, before Wimbledon, I probably would have signed for that."
In the women's quarterfinal played earlier on Arthur Ashe, Karolina Pliskova crushed Ana Konjuh 6-2 6-2.