Federer, 37 and bidding for his 101st career title, received a walkover into the final, where he will play Dominic Thiem, a 7-6 (3) 6-7 (3) 6-4 victor over Milos Raonic in Saturday's only semi-final.
Rafael Nadal withdrew from his BNP Paribas Open semi-final with Roger Federer, allowing the Swiss great to reach his ninth Indian Wells final. 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. "The way he came up was very clay-court based, and I was apparently very grass-court based, and we both found our ways also on the other surface", Federer said.
"I warm up today in the morning, and I felt that my knee was not enough good to compete at the level that I need to compete", he said.
It's particularly devastating since Nadal was looking forward to a relatively healthy 2019 campaign after coping with multiple injuries previous year.
Nadal choked up discussing his withdrawal last fall, and he appeared near tears on Saturday. Nadal didn't drop a set in reaching his fifth Australian Open final, where he lost to Novak Djokovic.
Just hours earlier Federer had looked forward to the chance to take on a healthy Nadal, after similar knee trouble spelled the end of the Spaniard's US Open campaign last year, and his US Open campaign last year.
He underwent surgery on his ankle to remove an intra-articular loose body in November and only resumed training in December.
While Nadal said he feels knee pain "almost always", in the face of this latest setback he insisted: "My goal doesn't change".
"It's tough for me to accept all these things that I'm going through in my career", the 32-year-old said, BBC Sport reported. "They warned me they were going to put me on at 11.00 (a.m.)".