Meanwhile, top seed Stan Wawrinka also made it to the last four after registering 4-6, 7-5, 6-2 victory over American Sam Querrey in their quarter-final clash.
The last time he reached an ATP Tour final was in 2010, when he was beaten by Frenchman Gilles Simon at the Moselle Open.
After losing the first set to qualifier Zverev, the older brother of Alexander Zverev who stunned Novak Djokovic in the Rome Masters final, three-time Grand Slam victor Wawrinka needed 2 hours 20 minutes to seal victory.
Second seed Nishikori dropped the first set to Kevin Anderson and then saved three match points in a decisive tie-break before triumphing 2-6 6-4 7-6 (8-6). Zverev opened up a 4-2 lead and routinely held on to his serve book a ticket for the final. Still, he soon created a second match-point chance with a forehand crosscourt service return for a victor.
"It was a great week for me here in Geneva", said Zverev.
Reaction to the death of music legend Gregg Allman
Cher, to whom Allman was married for four tumultuous years in the 1970s, used pet names and a broken heart emoji to pay tribute. The rest of the band was stricken but carried on and put out another well-regarded album, " Eat a Peach ".
In Thursday's other quarter-final, Zverev eased past fifth-seed Steve Johnson 6-4 7-5 in a match that lasted an hour and 34 minutes.
Earlier, Zverev wasted two match-point chances on Nishikori's serve before breezing through his next service game to clinch with a backhand volley victor. He (Anderson) had more chances, but I served a little bit better in the end. "It's important to win some matches like this", Sport24 quoted Nishikori as saying.
World No. 1 Andy Murray is battling to recover from illness before the French Open begins on Sunday, according to British media reports.
Zverev, 29, stunned the tennis world at the Australian Open when he beat World No 1 Andy Murray before losing to eventual victor Roger Federer.
