Berdych, who beat the virtually unstoppable and then six-times champion Roger Federer in the Wimbledon quarter-finals in 2010, had not beaten Nadal in 17 successive matches, tied for the record as the longest losing streak to another player.
The seventh-seed started like a runaway train against the 14-times grand slam champion, forcing him deep behind the baseline and painting the tramlines as every shot he attempted appeared to come off.
Berdych won the opening set for the first time in a run of seven matches against Nadal, then swept through the second in 25 minutes and despite a third-set fightback by the Spaniard, the damage was done and the Czech moved into a semi-final against either Andy Murray or Nick Kyrgios.
"I was definitely ready for it," Berdych said in a courtside interview. "I set up my plan pretty well and stuck with it through the three sets.
"I was expecting a tough battle but I was ready for everything and that was the difference."
Third seed Nadal had said prior to the tournament that he doubted whether he was mentally or physically ready to challenge for the title after injury and illness hampered the second half of 2014.
The 28-year-old Spaniard also suffered from dehydration, cramping and upset stomach to overcome qualifier Tim Smyczek in the second round but had looked imperious in his destruction of 14th-seed Kevin Anderson in the fourth round.
Nadal was clutching at his hamstring throughout the early stages of the match and did not seem at his usual pugnacious scrambling best, though Berdych had also upped his aggression level and used his booming serve to maximum effect.
The Spaniard recovered in the third set and saved two match points at 6-5 to force it into a tiebreak before Berdych sealed it on his fourth match point to advance into his second successive Melbourne Park semi-final.
(Additional reporting by Ian Ransom; Editing by John O'Brien)
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