Nadal was set to play against Filip Krajinovic in the last eight this afternoon but has withdrawn from the tournament and is now a doubt for London.
Nadal beat Hyeon Chung in the second round to guarentee he would finish the season as world No1 but he picked up an injury in the Pablo Cuevas match yesterday.
He needed the doctor on court before continuing and has now pulled out of the tournament.
Nadal did say he felt OK after the match and was looking forward to London, but his place at the ATP Tour World Finals later this month is now uncertain.
“The way that I am today I do not see myself playing three more matches,” he said after his withdrawal.
“The knee is always bothering a little bit but sometimes it’s worse.
“For me it’s not about London it’s about longer term.”
He will undergo treatment to try and be ready but it looks a long shot at this stage.
And when pushed on London he said he wasn’t ready to discuss whether he will be ready to play.
“I understand the question of course but I cannot talk about London now,” he said.
“I am now sad to pull out from here. I feel at home here so for me it’a very tough day.
“The only thing I can say is I’m going to do my treatment and try my best to be playing in London but I cannot talk about this now because it’s a day that is tough enough for me to have pulled out from here.”
Tennis analyst Annabel Croft suggested he was struggling to serve in the Cuevas win due to his knee.
Croft said: “I have no idea how much that knee was affecting everything. He came up with seven double faults and some of those balls were dribbling halfway up the net.
“You have to think that was because he couldn’t push up from that leg. He was different to the player that started the match.”
However yesterday Nadal did say: “I don’t want to talk about the knee but about the quarter final.
“I am in the most important city [Paris] of my life, I am not taking risks, I just play.
“Of course I will play in London!
“I don’t worry to play tomorrow at 3.30 pm. The rest is not a problem for me.”
Nadal has secured his status as the world No1 for the end of the season – and will become the oldest man to ever to do so – after winning six titles and two Grand Slams this season.
He won the China Open in Beijing and reched the final in Shanghai – losing to Roger Federer – and credits the Asian swing as a pivotal time for his season.
He had already been at No1 since August after winning at Roland Garros and then won the US Open.
But in Asia he shored up his status with Federer only playing one of the events before winning at Basel.
He said: “When the opportunity (to end the year at No1) presented itself, it became my goal,” Nadal said.
“The Asian swing was very important for me, because the points I gained during that time were valuable.”