The latest battle of big servers at the O2 resulted in a 7-6 (5) 6-3 victory for German Zverev, ending Isner's debut in the tournament at the group stage.
After 40 minutes of hammering their 130mph-plus missiles past each other, the first set went to a predictable tie-break which Zverev edged.
Dropping that set meant Isner knew he would be eliminated, but the American battled on gamely until Zverev eked out the match's solitary break of serve in the eighth game of the second set before sealing victory.
The dream final match-up between Federer and Novak Djokovic at London's O2 remains a tantalising prospect, but not if 21-year-old hot-shot Zverev has his way.
"It's obviously great getting to the semi-finals. But the tournament isn't over," he said.
"I am in the semi-finals. There's only good opponents left. There's only the best in the world.
"I'm playing Roger, which is going to be a very difficult but hopefully very nice match. We'll see how far I can go."
World number one Djokovic will face South African debutant Kevin Anderson, the man he beat in this year's Wimbledon final, in the other semi-final.