Defending champion Nadal has not been at his dominant best on his favoured clay this year, losing in the quarter-finals in Monte Carlo and Barcelona.
However, he had a relatively easy ride against the outclassed Czech sixth seed, a player he has now beaten on 18 occasions in 21 meetings on all surfaces and 17 times in a row.
Nadal broke Berdych's serve three times without losing his own and, with Roger Federer and Novak Djokovic withdrawing and Andy Murray knocked out on Thursday, remains firmly on course for a fourth Madrid Open crown.
David Ferrer, the fifth seed, beat unseeded Latvian Ernests Gulbis 7-6 (7-3) 6-3 to join his compatriots in the semis.
Ferrer next faces 10th seed Kei Nishikori who will become the first Japanese to break into the world's top 10 after he progressed to the last four with a 6-4 6-4 victory over Spain's Feliciano Lopez.
The last Asian male to reach the top 10 was Thailand's Paradorn Srichaphan in 2004.
Nadal said his performance was probably his best of the clay season, good news for the Mallorcan as he gears up for a tilt at a record-extending ninth French Open crown later this month.
"It was a match with a lot of intensity and perhaps it was my toughest match until now in the tournament," he told a news conference.
"To make it to the semi-finals for the first time in the clay season here in Madrid is great news for me," added the 27-year-old who is chasing a 63rd career title and a 44th on clay.
"I just managed to go over a barrier in the quarter-finals with a difficult opponent. I've been two weeks without doing that and I'm happy.
"Now I just need to make an extra effort. I have to keep on going along the line that I've been going which is each day to get a little bit better," said Nadal.
Bautista, ranked 45th, had never reached the last eight of a Masters event and continued his dream run with a 6-3 6-4 victory over Murray's conqueror, 46th-ranked Colombian qualifier Santiago Giraldo.
A promising soccer player in his early teens, the unheralded Bautista has two top 10 wins this year, defeating number five Juan Martin Del Potro at the Australian Open and Berdych in Indian Wells, California.
"I think Rafa is favourite no matter where he plays," said the 26-year-old Spaniard. "I will try to have the best match I can."
Bautista added he had grown in confidence this season after good results in New Zealand, Australia and the United States.
"My way of striking the ball is that maybe I strike it a little bit more flat than normal," he said.
"Every round I make is an extra motivation. Especially making it to the semi-finals and playing against Rafa."
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