The 18-year-old easily took the first set, lost the second on a tie-break before sealing victory over the Wimbledon finalist on his third match point in the third-set tie-break.
Felix Auger-Aliassime said that he is feeling positive about where his game is despite the 21-year-old losing to Daniil Medvedev in the US Open semifinal.
Don't think I played my best tennis: Daniil Medvedev after win against Felix Auger-Aliassime in US Open
Daniil Medvedev hoped he could win the US Open title this time around after losing the title match against Rafael Nadal in 2019.
Beating No. 2 Daniil Medvedev on Sunday for the title will allow Djokovic to be the first man since 1969 to complete a calendar-year slam and collect his 21st grand slam, most among men.
Zverev rallied from a set down to beat Djokovic in Tokyo, then went on to win gold. They meet again on Sept 10 in the US Open men's second semifinal after Daniil Medvedev faces Felix Auger-Aliassime.
Djokovic is now two wins away from the first calendar-year Grand Slam in men's tennis since 1969, along with a men's-record 21st major championship overall.
With no players from the United States left to pull for, U.S. Open fans are adopting their neighbours from the North - Leylah and 21-year-old Felix Auger-Aliassime for the women's and men's titles.
Felix Auger-Aliassime has now reached the second week at the Australian Open, Wimbledon and US Open this season.
Stefanos Tsitsipas beats Felix Auger-Aliassime to set up Cincinnati semis clash against Alexander Zverev
Stefanos Tsitsipas defeated Felix Auger-Aliassime after two hours and 12 minutes to reach the semis in Cincinnati.
First task, though, for Matteo Berrettini is to cheer for his girlfriend Ajla Tomljanovic later on Tuesday in her first Grand Slam quarter-final when she plays fellow Australian Ashleigh Barty.