Spaniard Ferrer's modus operandi has been to drag opponents into endless rallies until they succumb via fatigue or a loss of focus, but Nishikori showed himself up for the scrap and won most of the longer exchanges.
Nishikori blew two match points but closed out the third when Ferrer netted a forehand to seal the win in two hours and six minutes.
Japan's number one will meet defending champion Stan Wawrinka for a place in the semi-finals.
(Reporting by Ian Ransom; Editing by Sudipto Ganguly)
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