Young, ranked No. 81 in the world, won a first-set tiebreak and dropped the second before holding on in the third set for a 7-6 (5), 3-6, 7-6 (6) victory at The Racquet Club to reach the semifinals.
Young let a triple-match-point opportunity slip away at 6-3 in the third-set tiebreaker, but after Isner won three straight points to tie it at 6-6, Young won two points to finish off the upset.
"With him, it comes down to a couple points here and there, and I was able to get those today and I was able to hold my serve for the most part of the match and just defend well," Young said.
The 27-year-old Young beat Isner, the No. 2 seed who is ranked No. 23, for the first time in four tries in their first meeting since 2014. Isner was the last remaining seed in the event.
"He's beaten me every other time we've played so I wanted to get at least one," Young said. "I'm just happy I was able to stay focused, come through, deal with a little tightness and still prevail. So I'm happy with the performance."
Young will face another American, Ryan Harrison, in one semifinal. Harrison defeated Damir Dzumhur of Bosnia-Herzegovina 6-3, 6-4 in a quartefinal match that ended late Friday night.
Upsets have prevailed in the tournament. None of the top seeds reached the semifinals.
Mikhail Kukushkin powered his way into the semifinals with a 6-0, 6-4 victory over fourth-seeded Steve Johnson.
The Kazakhstan qualifier, ranked No. 103 in the world, has been rolling this week, winning three matches while losing only 14 games along the way. The semifinal berth is his first in an ATP World Tour event since January 2015 in Sydney, Australia.
The win over Johnson evened Kukushkin's career record at 2-2 against the American.
Johnson bounced back after being blanked in the first set, taking a 4-1 lead in the second before Kukushkin kicked it into another gear and reeled off five consecutive games to finish off Johnson in 70 minutes.
Kukushkin's semifinal opponent will be Nikoloz Basilashvili, who defeated qualifier Matthew Ebden of Australia 7-6(3), 6-4.
Basilashvili fell behind 4-1 in the first set before rallying and then trailed 3-2 in the second set before he rallied from a break down in the match that last 1:44.
The Georgian had advanced to the quarterfinals by knocking off top-seeded Ivo Karlovic on Thursday. Basilashvili reached his second consecutive semifinal on the tour.