Nadal had been set to play longtime rival Roger Federer later Saturday.
Nadal's knee appeared to flare up in his quarter-final win over Khachanov on Friday, where he twice received treatment from his trainer, with the Spaniard stressing after the match he would need to assess the injury ahead of the match on Saturday. The first semifinal begins at 2 p.m. EST.More news: NBS: China's economy remains stable, investment accelerates in Jan-Feb
It would have been the 39th career meeting between Nadal and Federer, who advances to Sunday's final in pursuit of a record sixth title at Indian Wells.
"But at the same time, in the other hand, I went through fantastic moments and still going with that feeling a lot of times". I thought the match was definitely on. They've faced each other only four times, most recently at the ATP Finals in November, which Federer won, and three times in 2016. However, Nadal soon texted him it wasn't going to happen. "And at the same time, two players with a good relationship after all the things that we went through in our careers, competing for the most important things", he said.
Federer said he might not feel quite the same tingle of anticipation as fans at the prospect of facing Nadal, but he acknowledged that their clashes always raise the stakes.More news: Theresa May in final Brexit push
But he couldn't make a dent in Federer's serve and one break in each set was all Federer needed to seal the win after an hour and 14 minutes.
In his post-match press conference, Nadal admitted to reporters that he would have to see how he felt the following day. "Of course my goal and my idea is to be ready for tomorrow", Nadal said. Federer started for real on tour in 1999, and by 2003, when Nadal was becoming a force, Federer was already flirting with being No. 1.
"I know every one we have now could be our last", Federer said. It's one of the most handsome centre courts that we have in the world, it would have been very special. "I hope we can have many more to come".More news: New Zealand pledges reforms as relaxed gun laws scrutinized