World No 2 Nadal took a 5-0 record over the Russian into their match and if the Spaniard extends that dominance it will set up the 39th meeting between him and Federer - their fourth at Indian Wells.
After 38 career meetings, Nadal leads the series 23-15, but Federer holds a slight 11-9 advantage on hardcourts.
And despite cruising through the early rounds, Nadal was unable to recover from Friday afternoon's physical match against No. 12 Karen Khachanov, a match that required two tiebreakers - and two visits from the trainer to attend to his right knee - for Nadal to win in straight sets.
The 37-year has eased through the draw without dropping a set and having made history by joining Jimmy Connors in the 100 club with his title success in Dubai a couple of weeks ago - he is on track for 101 when he faces either Raonic or Thiem in Sunday's final. The first semifinal begins at 2 p.m. EST. I thought the match was definitely on.
The Swiss great has won the last five in the series, but says that's of little significance now that it has been nearly a year and a half since their last meeting in the Shanghai Masters final in October 2017. 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.
"It's very awkward but it's a big letdown because I know the anticipation was there from the crowd and especially also from us players". They've split wins, with Federer winning both of their hardcourt matches and Thiem winning once each on grass and clay.
"It's about what it means for me to have to pull out in a tournament that I love so much like this one, and in the semi-finals after playing well during the whole tournament". I really hope not. "A lot has happened in those 18 months... you can't just copy/paste and play exactly the same thing again", said Federer. It's one of the most attractive centre courts that we have in the world, it would have been very special.