Nadal, who had already sealed his berth, helped seventh seed Stanislas Wawrinka of Switerland to qualify for the semifinals. (Agencies)
Berdych needed to beat Nadal to ensure his spot in the last four, reported Xinhua.
"Stan came to the locker room and said good luck. I said I would try my best. It's a good result for Stan. He's good friend of mine," said Nadal.
Nadal completed a 6-4, 1-6, 6-3 victory over Berdych in one hour and 50 minutes. The win means that he will face fourth seed Juan Martin del Potro or sixth seed and six-time former champion Roger Federer in the semi-finals on Sunday.
In the day's other match, Wawrinka fought back from one set down to beat third seed David Ferrer 6-7 (3-7), 6-4, 6-1.
Ferrer, 31, who lost all three matches, said, "I played a lot of tournaments. I played seven tournaments in seven weeks."
He added, "I made the final in Stockholm, final in Valencia, final in Paris, and three matches here. It's too much. But now I know it's too much. Before, I never knew it. I made three finals in three weeks."
Nadal has won 10 titles from 13 finals since returning from a seven-month injury lay-off in February. He has compiled a 23-4 record against Top 10 opponents in the ATP Rankings.
Nadal, who had already sealed his berth, helped seventh seed Stanislas Wawrinka of Switerland to qualify for the semifinals.