The Spaniard, out from last summer until February with a debilitating knee injury, raised eyebrows when electing to return to the hard-court circuit for Indian Wells.
But he showed no sign of his absence in a scintillating display of power and mobility against a sluggish Federer, who was far from his best but would probably have struggled against Nadal anyway.
Nadal broke his opponent once in the first set, but in truth he missed some opportunities to bury the Swiss.
He continued his dominance with back-to-back breaks at the start of the second set, as the world number two Federer looked a shadow of the Spaniard who has slid down to fifth.
Federer did have a mid-set resurgence, breaking back at one point, but Nadal broke for a third time and held easily to close out the win.
Nadal has to play world number six Tomas Berdych for a place in the final on Sunday.
The result means Nadal improves his career record against the Swiss to 19-10; this was the first time they had met at the quarter-finals of a tournament, as the former world number one’s lower ranking starts to throw up some interesting draws.
"After seven months away, I am very happy to be in the semi-finals here," a beaming Nadal said courtside.
"I played great the first set. I played a fantastic first set, in my opinion. The second set I think Roger didn't fight as usual. Probably he had some problems and he didn't feel comfortable enough to keep fighting.
"The first set was a good match, in my opinion. Both of us tried to play our best. I played much better than yesterday.
"Always it is a very, very special match against Roger, the best player in history. I feel like it is a classic match whenever we play."
Asked what had pleased him most about his game, Nadal replied: "My movement tonight was much better than yesterday. I played longer than yesterday.
"I had a good feeling on my forehand, even if I had a few mistakes with my backhand in the second set.
"Sometimes today I am not able to play all the shots with my forehand that I used to be because I am not that fast yet to do it. That's why the backhand today is very important."
Federer - who came through a three-setter with fellow Swiss Stanislas Wawrinka in the fourth round - has been feeling a twinge in his back recently, and it showed as he struggled to move freely, while missing a number of backhands he would ordinarily have buried.
When asked how much the problem affected him against Nadal, Federer replied: "Same as against Stan.
"I am happy to be out there and able to compete. It's always an issue and doesn't work against a guy like Rafa. But I don't want to undermine his performance here."
Soon enough Federer was broken as the resurgent Nadal’s power and accuracy, particularly on his forehand and off the high-bouncing hard-court, showed no sign of having been diminished by seven months out injured.
Federer’s defence was uncharacteristically weak and he was almost broken a second time as Nadal looked to claim the opening stanza, the Swiss saving a couple of break points; in the end the Spaniard had to settle for serving it out to 6-4.
Nadal was playing as superbly as Federer was toiling, his forehand as unyielding as the Swiss’s backhand was erratic.
Federer’s forehand was starting to suffer too, and he was broken to love at the start of the second.
The 17-times Grand Slam winner’s decision making was poor at times, coming to the net when he should sit, trying drop shots with Nadal well-placed. He struggled to get points on the board against serve and was broken a second time as he appeared on the brink of collapse.
But there was a resurgence, the Swiss finding something close to his peak form in retrieving one of those breaks, one point of baseline bullets, lobs and gets a joy to behold.
He went close to erasing Nadal’s double break, but the Spaniard held and with Federer fading badly, there was only one winner on a sweaty California evening.