The world number one took an hour to claim the first set after a difficult contest against his Spanish opponent, where tight rallies dominated the opening set.
While the Serbian appeared slightly weary during the initial stages of the quarter-final, a number of sensational forehand shots edged the scoreline in Djokovic's favour, resulting in the capture of the first set.
Ferrer refused to give up but failed to snatch the major points, which led Djokovic to break the 29-year-old's serve in his opening game of the second set.
The fifth seed began to come into his own and level the set 2-2 before taking the lead three games to two. However, Djokovic's slight dip didn't stop him from executing some vital shots to equal the scoreline.
With the Serbian pro seeming to hang on in the closing stages of the second set, Ferrer managed to force through a tie-break but couldn't overcome the number one seed, who took a two-set lead after two hours and 15 minutes of play.
While Djokovic struggled midway through the match, there were no doubts over his form in the third set as he stormed to victory and a semi-final spot.
The 24-year-old has to get past the British number one for a chance to retain his Australian Open title.