The tenacious Ferrer pushed Djokovic hard, manoeuvring him around the court, but the world No 1 stepped up his game when it mattered to win 6-4, 7-6 (7/4), 6-1 in 2 hours and 44 minutes.
Looking tired at the end of the first set, Djokovic produced a stunning blind, backhand winner at full stretch from the back of the court early in the second, breaking in the first game.
He looked in trouble when he grimaced in pain, clutching his left hamstring as Ferrer levelled at 2-2 but he did not appear to be restricted, going on to take the tiebreak and seize a 2-0 lead.
"Already after a couple of games I was feeling it was going to be a long match," Djokovic said.
"There was a big mental advantage to getting two sets up," he said, adding that he had stepped up his aggression as the match wore on and it paid off."
When quizzed about a possible fitness issue afterwards, Djokovic was giving nothing away.
"You have to hang in there, David is a great competitor and he always makes you hit every shot," he said. "I wasn't feeling very fresh."
Djokovic will take on Murray in Friday's semi-final, a repeat of last year's final which the Serb won in straight sets to clinch the first of three grand slam titles last season.