It took over an hour for Berdych to clinch the first set after a controversial moment between Nadal and a line judge at the Rod Laver Arena. The 25-year-old attempted to challenge a shot from his opponent during a tie-break but due to the lateness of his call, was refused by the umpire.
The world number two claimed that he was waiting for the female line judge to confirm that the shot before requesting a challenge. The line official in question was swiftly replaced after Berdych took a one-set lead in Melbourne.
Nadal recovered from that setback to level up the scores following another tie-breaker. On this occasion, the former world number one came out on top 8-6.
Both players traded breaks in the third set, before Nadal's second break proved to be decisive as he went on to take a 2-1 lead with a 6-4 success.
Mallorca-born Nadal broke Berdych early in the fourth set to open up a two-game advantage. Berdych was unable to produce a comeback and was eventually broken again as Nadal wrapped up a 6-7 7-6 6-4 6-3 victory.
The Spaniard will now face Roger Federer for a place in the final.