The top-ranked Nadal had lost his previous two quarterfinal matches on clay for his worst run on the surface in a decade. But buoyed on by a partisan crowd, Nadal overpowered Berdych 6-4, 6-2 to advance at the Magic Box.
"I brought great energy and intensity to it and that's the best news, that it's my best (on clay) yet," Nadal said. "The things that, historically, I've done well on this surface I managed to do them again today."
Nadal has been improving with every match in Madrid after losing at the quarterfinals stage in preceding tournaments in Monte Carlo and Barcelona.
But he showed no sign of the nerves that had uncharacteristically crept into the game of the most successful clay-court player ever as he pushed Berdych to the corners and punished him with a powerful forehand that accounted for 16 of his winners.
"My play is good when I'm hitting my forehand well, especially on clay," said Nadal, who is vying for his third title in the Spanish capital. "In Monte Carlo I used my backhand more and not my forehand, and when I have to hit five or six backhands in a row it doesn't help my game."
Berdych, who dropped to 3-18 against Nadal, couldn't keep up in the hot sun beating down on Manolo Santana center court.
The top-ranked Williams has had her left thigh heavily bandaged this week and said she injured it during a first-round victory over Belinda Bencic on Sunday.
The withdrawal gave 2011 champion Petra Kvitova a walkover and a spot in the semifinals.
Sharapova reached the semis after she rallied to beat Li 2-6, 7-6 (5), 6-3.
Li was in control until she failed to convert two break points in the 11th game of the second set. Errors then began creeping into the Australian Open champion's game as Sharapova evened the match.
After an exchange of breaks in the third set, the ninth-ranked Russian broke again and then held serve to win on Li's 43rd unforced error.
"It really could have gone her way today. You know, it was just a matter of a few points in the second set," said Sharapova, who came through despite seven doublefaults. "I was down, I didn't play a great first set, and I found a way to get myself in a position to be in the third."
Information from The Associated Press was used in this report.