Ferrer, the sixth seed, outgunned Murray 6-4, 6-7 (3-7), 6-3, 6-2 to progress to the final four, while Nadal got past another compatriot Nicolas Almagro 7-6 (7-4), 6-2, 6-3.
The result moves Nadal closer to a record seventh French Open title, while it earns him his 50th ever victory at Roland Garros.
Nadal said: “My serve worked really well, and (Almagro) had one mistake, one important mistake with the forehand.”
He added: “I was just trying to wait for my moments. He had some good moments and he was hitting the ball hard, but I had my chances, too.’’
Meanwhile, Murray’s defeat continues his long quest to win a Grand Slam.
“(Ferrer) had his chances and converted them. He’s solid and consistent and if you don’t convert opportunities against him, the games become longer and the pressure builds on you,” Murray said.
Murray added he felt he’d been knocked out by a better claycourt player and favoured Nadal to win the title.
“I think the four best claycourt players in the world are left in and whoever plays best will win,” he said.
“I probably have to favour Rafa slightly, but everyone is playing very, very well.”