Federer, fresh off a remarkable 100th career title in Dubai, remains tied with Novak Djokovic for the most Indian Wells victories with 5.
"I warmed up today and I felt that my knee was not good to compete at the level I needed to compete in semifinals", Nadal said in a statement.
"I don't have doubts today that I will be ready for Monte Carlo", Nadal said.
In a situation not often seen in football stadiums around the world, Real Betis fans joined along with Barcelona fans to cheer Lionel Messi after the Argentine superstar produced another breathtaking display, scoring a hat-trick in their 4-1 La Liga victory.
Thiem prevented Federer winning a record sixth Indian Wells title, beating the Swiss great 3-6, 6-3, 7-5 to claim his first ATP Masters 1000 crown. Federer sealed the first set with a service victor after Thiem handed the set to the Swiss on the back of break points.
Canadian teenager Bianca Andreescu rallied past No. 6 Elina Svitolina 6-3, 2-6, 6-4, winning on her fourth match point to reach the biggest final of her young career.
Nadal choked up discussing his withdrawal last fall, and he appeared near tears on Saturday.
Thus, Thiem has become only the seventh different Indian Wells champion since 2002 and also the 67th different Masters 1000 victor since the series was established in 1990.
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Her most dominant win during the 12-day tournament came in the quarterfinals, a 6-0, 6-1 rout of two-time major champion Garbine Muguruza. "I didn't feel like I played bad, either". However, Nadal soon texted him it wasn't going to happen.
"I feel like he had to come up with the goods, and it did feel like to some extent it was on my racquet", Federer said.
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 you feel that way, you take it more positively".
"It's been a great week for me, even though it didn't work out", Federer said. Federer won just two more games in the set.
Thiem has never won a Masters 1000 title, losing in two previous finals.
It looked like Federer lost some momentum while serving in the final set, especially when Thiem broke him.
'I think that was a really important five minutes in the match, ' Federer said.