Nadal was forced to call it a day at two sets down against Juan Martin del Potro during the semi-final in the early hours of the morning.
The Spaniard has now had to withdraw from two Grand Slams this year due to injury as his knee problems continue to torment his career.
He twice needed medical attention before conceding at Flushing Meadows, sending Del Potro into the final for the first time since 2009 where he will face Novak Djokovic.
“It was difficult for me to keep playing. I was in too much pain,” said the 32-year-old Spaniard.
“It was one player playing and one on the other side of the court. I hate retiring – but to stay one more set out there playing like that is too much for me.”
He was visibly emotional on court knowing his chance of an 18th Grand Slam was gone.
And in the press conference after he was asked if playing on hard courts was difficult because of his condition.
All the Spaniard could muster in response was: “It’s okay” before tearing up.
Nadal won the US Open last year and has won four slams on the hard courts in New York and Australia.
But the 32-year-old insists he has to constantly manage his body and stresses the current injury is not one that will need much recovery, just careful management.
“Just about do treatment,” he said when asked about the recovery process.
“Is not an injury that tells you three weeks off and you are back. Is not an injury that tells you six months off, you are back.
“Is maybe an injury that in one week you feel better, is an injury that maybe in six months you don’t feel better.
“I know what is going on with the knee. But the good thing is I know how I have to work to be better as soon as possible because we have a lot of experience on that.
“I am sure will not be the six months off. I was just making a comparison. Is not an injury like when you break something, something like this.
“It is an injury that is a tendinitis. Then is a decision about yourself, about if you want to wait till you feel almost nothing or you want to keep going with pain, so…
“Is not the moment to think.”
Nadal emerged back at the top of tennis last year winning the French Open and the US Open, his first slam victories in three years.
He remains in battle with Roger Federer at the top of the game but will not add to his slams for the year after winning at Roland Garros again.
He is due to play in the Davis Cup final next week when Spain take on France, but his participation is surely in doubt following the latest retirement.
His next scheduled tournament is Beijing at the start of October.