The Montreal native was a huge attraction in his hometown at a pre-US Open event missing both world number one Jannik Sinner and 24-time Grand Slam singles champion Novak Djokovic.
Auger-Aliassime's pullout sends opponent Titouan Droguet into the third round.
"I started having pain Monday," Auger-Aliassime said. "It was quite sudden. I was training here for two weeks and I had zero problems. So it happens sometimes. It has happened for me in the past.
"The timing is tough, right, for it to happen here. Then I was lucky to get an extra day to prepare, as I was ready to play Tuesday night.
"I thought that day by day things would get better, but I tried to go on court today.
"I tried to warm up and then I basically couldn't serve really, so it was impossible for me to think about even competing."