Another loss, and Berdych would have been the first man in the 47-year open era to lose 18 consecutive matches to a rival.
Instead, he joined Jo-Wilfried Tsonga as only the second man to claim the grand slam scalps of Nadal, Roger Federer, Novak Djokovic and Murray.
Widely regarded as the best player yet to win a major, the 29-year-old now believes he can break through at Melbourne Park.
"I'm ready," Berdych said. "I'm feeling strong and confident and I want to go all the way."
Nadal came into the tournament insisting he wasn't a serious title contender after playing only eight matches since Wimbledon because of back and wrist injuries and an appendectomy in October.
He dodged a bullet in the third round against lowly-ranked American qualifier Tim Smyzcek but appeared to be working his way into the championship, winning his next two matches in straight sets.
But Berdych brutally exposed his lack of match toughness, striking 46 winners to 24 on Rod Laver Arena.
A semifinalist in Melbourne for the first time last year, Berdych was on top from the outset.
Nadal gave him the first break of the match with a string of unforced errors in the fourth game.
Berdych broke Nadal for a second with a powerful backhand cross-court winner to take the opening set after 35 minutes.
It was only the second time in his nine-year losing streak against Nadal that he'd won the first set against the Spanish superstar.
But unlike the previous occasion, in the quarter-finals in Melbourne three years ago, Berdych kept the pressure on, giving Nadal his first 6-0 set loss since 2006 and resisting a third set comeback to triumph.
