The world No2 had looked set to return to competitive action at Flushing Meadows after hitting the practice courts all week.
But Murray waited until Saturday afternoon to decide his hip had still not fully recovered enough to feature in the Grand Slam.
Had the Scot pulled out prior to Friday’s draw, Roger Federer would have moved up to number two seed and he and Nadal would not have been in the same half of the draw.
But now both Federer and Nadal could face-off in the semi-final of the US Open.
And Nadal, who progressed into the second round after beating Dusan Lajovic 7-6 (8/6) 6-2 6-2, was mystified by Murray’s decision.
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“It was a little bit strange that he retired just the morning after the draw was made. It was something that is a little bit strange and difficult to understand.
“Normally you want to keep practising, keep trying until the last moment. You don’t retire Saturday morning. You retire Monday morning or Sunday afternoon. If not, you can do it before the draw.
“That’s why I say it’s strange. But of course he has his reason, and for sure the only news, and the negative news, was that he will not be playing here.
“Injuries are bad for everybody. I know better than all of them.
“So I wish him fast and good recovery. That’s the most important thing.”