The Spaniard looked in discomfort during the match and only had a brief practice session on Saturday.
Nadal's withdraw was a disappointment for sure, but to spend too much time focusing on the past would be disrespectful of what's to come Sunday.
As the Spaniard tennis phenom, Rafael Nadal announced the sad news for the tennis followers worldwide by calling off the 39th "Fedal" rendezvous and Federer without any hassles sailed into finals of the Indian Wells 2019.
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Nadal, who has struggled with knee injuries throughout his stellar career, was the second high-profile player to withdraw from the tournament. "I can not guarantee how I'm going to wake up tomorrow morning".
Nadal said he hoped to be ready to battle again with Federer, but with a pragmatism born of hard experience he couldn't help but hedge.
"I wanted to try my best to be competitive today", a dejected Nadal said. They've split wins, with Federer winning both of their hardcourt matches and Thiem winning once each on grass and clay.
Nadal trailed 6-5 before Khachanov's forehand error forced the second tiebreaker, which Nadal dominated to close out the match that lasted just over two hours.
"When Rafa is healthy, especially in a place like here in Indian Wells where he feels comfortable, he's clearly very tough to play", Federer said. "Roger was playing great in the crucial moments".