Nadal, the highest seed remaining in the event at No. 5, defeated the fourth-seeded Ferrer 4-6, 7-6 (7-3), 6-0. He improved his 2013 match record to 29-2.
Berdych downed Murray 7-6 (7-3), 6-4 and will take on Stanislas Wawrinka in the semifinals after Wawrinka outlasted Jo-Wilfried Tsonga 6-2, 6-7 (9-11), 6-4.
Ferrer failed to capitalize on two match points in the second set and lost for the 18th time in 22 meetings with Nadal.
"After missing his chance, David fell apart a little," Nadal said. "He lowered his intensity in the third set and I didn't have to do as much."
Nadal has reached the finals in all six of his previous tournaments this year, losing only to Horacio Zeballos in Chile and to Djokovic in Monte Carlo.