A day after the Spaniard collected his 300th career win on clay, he was unable to extend his winning run as compatriot Ferrer recorded a 7-6 (7-1) 6-4 quarter-final victory.
An even opening set saw both players break twice in the opening five games at the ATP 1000 event, but the set eventually settled down to a tie-break.
Ferrer was imperious in the shootout after losing the first point, reeling off seven in a row to move 1-0 ahead.
Nadal struggled to contain his opponent in the second set as the world number one lost his serve on two occasions to fall 5-2 behind.
With Ferrer serving for the match, Nadal showed his fighting spirit to claw the next two games back.
However, the world number six wrapped up the win as Nadal fired a backhand into the net, meaning Ferrer advances to face Stanislas Wawrinka in the semi-finals.
Australian Open winner Wawrinka sealed his spot in the final four with a 7-6 (7-5) 6-2 win over Canada's Milos Raonic.
Roger Federer booked his place in the semi-finals with the 950th win of his career, although he was made to work by Jo-Wilfried Tsonga.
After losing the opening set, Federer battled back to level the match before eventually completing a 2-6 7-6 (8-6) 6-1 win with a degree of comfort.
The world number four will face defending champion Novak Djokovic, who also survived a scare in his quarter-final.
Guillermo Garcia-Lopez, the winner of last week's Grand Prix Hassan II in Casablanca, took the opening set against the second seed.
However, the Spaniard was unable to maintain his form as Djokovic hit back to record a 4-6 6-3 6-1 win.