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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.
Left-hander Nadal, twice champion at Indian Wells, broke Berdych twice to take the opening set in just over an hour in blustery conditions on 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 Czech netted a backhand.
"It was a very important victory for me," the Spanish world number three said at courtside. "The conditions are always very nice here and it's amazing me for this feeling."
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 semi-finals," Ljubicic told reporters 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 played some great tennis and I felt really creative out there. Lobs, drop shots, volleys, winners, slices -- I felt I could hit the ball anywhere, you know.
"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.
