Fourth seed Marin Cilic leapfrogged Tomas Berdych to go ninth in the battle to qualify for the ATP World Tour Finals in London next month by fighting back to win 4-6 7-5 6-3 against qualifier Zverev.
Ninth spot will be sufficient for the world number 12 from Croatia to play in the lucrative World Tour Finals given that Rafael Nadal is ruled out due to injury.
Zverev claimed a stunning victory over Stan Wawrinka on Friday to become the first qualifier to reach the last four of this tournament since Marcos Baghdatis 11 years ago and the world number 72 threatened to claim another scalp a day later.
Cilic did not earn a single break point as he lost the first set, but took his only chance of the second to level the match and needed just one more in the decider to reach the final.
Zverev had seven opportunities to break, but Cilic thwarted the German outsider time and time again as he failed to hold just the once in a tight encounter.
Third seed Nishikori also came from a set down to avoid an upset, ousting Gilles Muller 4-6 7-6 (7-3) 6-3 in the first semi-final.
World number five Nishikori will now look forward to the 20th final of his career – and his fifth of the season – as he eyes only a second title in 2016.