The No. 2-ranked Nadal and No. 3-ranked Federer are on the same half of the draw at a major for the first time since 2005.
Federer beat U.S. Open champion Juan Martin del Potro earlier in three sets to advance to the Australian Open semis for the ninth consecutive year. He has won four of his 16 Grand Slam titles at Melbourne Park.
Nadal won the Australian title in 2009, but lost in the quarterfinals in 2010 and '11.
It was Nadal's 10th consecutive win over Berdych, a sequence including the 2010 Wimbledon final.
The Nadal-Federer rivalry is considered one of the most significant in the sport today. The two players held the top two rankings on the ATP Tour from July 2005 until 14 September 2009, when Nadal fell to World No. 3, and and they have met in eight Grand Slam finals.
Their 2008 match at Wimbledon is considered by many tennis analysts as one of the greatest matches of all-time.
Djokovic and Federer are the only players to defeat Nadal in more than one Grand Slam final and Djokovic is the only player to beat Nadal in a Slam final on a surface other than grass.
Based on reporting by the Associated Press.