He was coming off two consecutive five-set victories — including over No. 3 seed Stefanos Tsitsipas in the third round — that made the 18-year-old from Spain the youngest man in the quarterfinals of New York's hard-court Grand Slam tournament since 1963 but also made it "really tough to recover."
Alcaraz retired from the match while trailing 6-3, 3-1 in Arthur Ashe Stadium.
"It's really tough to end a great tournament like this, but I had no choice," Alcaraz said. "First of all, I have to take care of my body."
The 12th-seeded Auger-Aliassime said he "really didn't see anything" during the match that led him to believe his opponent would need to stop.
The 21-year-old from Canada reached his first Grand Slam semifinal and will face Daniil Medvedev on Friday.