World number one Nadal, chasing a record-extending ninth Roland Garros title, had no answer to the fifth seed's pace on court Suzanne Lenglen in the first set.
But Ferrer, one of three men who have beaten the claycourt machine on his favourite surface this year, ran out of steam in the second before Nadal devoured him in the third.
Nadal won 10 games in a row - and 13 of the last 14 - to wrap up victory on his first match point, setting up a meeting with Wimbledon champion Andy Murray, who beat local favourite Gael Monfils 6-4 6-1 4-6 1-6 6-0 in the last eight.
"David on clay? He is one of the best players of the world. He gets better and better. I'm sorry for him today," Nadal reporters.
"In the first set I made too many mistakes with my backhand," he said.
Ferrer was on fire in the opening set, piercing Nadal's concrete defence with his devastating forehand.
Nadal, who has a 64-1 record on the Paris clay, realised in the opening set he was in for a dogfight.
At the end of a 31-shot rally, he unleashed one of his trademark forehands down the line and paused for a fraction of second as if certain it had done the job. But Ferrer retrieved the shot with a chopped forehand that landed in the open court, out of Nadal's reach.
Ferrer, as quick between his serves as Nadal is slow, took the set on his opponent's serve with a forehand winner into the corner.
Then, however, things started to click for the King of clay.
Nadal broke for 2-1 with a stunning backhand down the line. Ferrer had three chances to break back in the sixth game but could not convert them.
From then on, Nadal rolled on towards his 22nd win over Ferrer in 28 meetings.
He carries into Friday's semi-final clash a 14-5 record against Murray, whom he has beaten five times out of five on clay for the loss of two sets.
