The world number six had looked in ominous form, wrapping up the first set 6-3 and heading for a place in the last four.
Ferrer looked set to wrap up the match as he led 5-2 in the second set tie-break. However, Nishikori produced a late rally to snatch the set.
With both players looking to make a key breakthrough in the deciding set, it was the world number seven who broke the Spaniard in the ninth game thanks to some powerful groundstrokes and had the opportunity to serve out the match.
Nishikori then sealed his quarter-final victory against Ferrer, who misses out on an automatic place at the end-of-season ATP Finals in London.