No. 6-seeded Raonic moved on when his second-round opponent, Viktor Troicki of Serbia, retired with a right calf injury while trailing 3-0.
Berdych broke Falla once in each set without giving away a break chance, and closed their first meeting with his ninth ace at Ariake Colosseum. He notched his 50th win of the season.
The Czech, the 2008 champion here, is seeking his second title of the year after winning indoors in Montpellier, France, in February.
"The big difference between today and my first-round match is that I am feeling much better physically," Berdych said.