The Spanish left-hander came from 3-1 down in the second-set tiebreak, winning the last three points of the match at the Indian Wells Tennis Garden to book a place in the last four against big-serving Ivan Ljubicic.
Croat Ljubicic, who turns 31 on Friday, earned himself an early birthday present by powering past Argentina's Juan Monaco 4-6, 6-2, 6-1 earlier in the day to reach the semi-finals.
Third seed Nadal, twice champion at Indian Wells, broke Berdych twice to take the opening set in just over an hour on a blustery evening at the showpiece stadium court.
After the players traded service breaks in the seventh and eighth games of the second, the set went into a tiebreak, which Nadal clinched when the 19th-seeded Czech netted a backhand.
"I played really well, especially the first set," the Spanish world number three told reporters after beating Berdych for the sixth time in a row.
"The first eight, nine games of the match were at an unbelievable level, later the wind came a little bit and it was more difficult to play.
"I played aggressive with decision and that was the match," added Nadal, who has shaken off the knee injury that forced him to abandon his Australian Open title defense in January.
Former world number three Ljubicic unleashed 11 aces and 39 winners to wrap up victory in one hour, 47 minutes against Monaco on a hot afternoon in the California desert.
Ljubicic sealed the win by firing down a first serve at 138 mph that Monaco was unable to return, prompting the Croat to leap into the air and thrust his right arm skywards in celebration.
"It's a great win and a great present to have a day off just before the semifinals," Ljubicic said after reaching the last four in an ATP Tour event for the first time since his victory in Lyon in October.
"I got a phone call from my brother just after match. He said that in the Croatian time zone, I finish just a couple seconds before my birthday, so it's fantastic," he added with a broad grin.
"I'm playing fantastic tennis," said the Croat, who eliminated second-seeded Serb Novak Djokovic in the fourth round. "Now the key is to keep going." Monaco broke 6ft 4in (1.93m) Ljubicic in the seventh game of the match to take the opening set but the 20th-seeded Croat then took control with a deft mix of power and creativity.
He broke the Argentine's serve twice in both the second and third sets to become the first Croat to reach the last four at Indian Wells since Goran Ivanisevic in 1996.

Meanwhile, Jelena Jankovic rallied from a 2-4 second-set deficit to beat Alisa Kleybanova 6-4, 6-4 and reach the semifinals.
Jankovic won the final four games of Thursday's match, twice breaking Kleybanova, to extend her best showing of the year. Jankovic made the semifinals at Indian Wells in 2008, and went on to finish the year ranked No. 1 in the world.
"I haven't been playing well," she said. "So it's nice to get that feeling back and to be winning again and be in the end of the tournament again." At the start of the two-week event, the locker room was so crowded Jankovic could barely set her racket bag down. She arrived Thursday and found plenty of room.
"I like that feeling," she said. "I want to be at the end of the tournament where there's no one and there's only a couple of us standing. That means I'm doing well." Defending men's champion Rafael Nadal was to play Tomas Berdych of the Czech Republic in a night match. Nadal has beaten Berdych five consecutive times.
Ivan Ljubicic of Croatia defeated Juan Monaco of Argentina 4-6, 6-2, 6-1, setting up a semifinal against either third-seeded Nadal or No. 19 Berdych.
Ljubicic had his serve broken just once - in the first set - and won eight of the final nine games, helped by 11 aces.
After playing three consecutive night matches, Jankovic faced much different conditions during the day, with the sun in her eyes and the temperature in the upper 80s.
Kleybanova was within a point of taking a 5-2 lead on her serve in the second when the Russian double-faulted twice in a row and got broken.
Then Jankovic held at 4-4 and owned the momentum the rest of the way.
"Against Kleybanova it's really not easy to play your game because she plays those really flat shots and you never know where she's gonna hit it," Jankovic said. "It can throw you back at times."