The Canadian pulled out of the Lyon quarter-finals last week with a shoulder problem and revealed that he had also been unwell during that tournament, with a similar issue hampering his progress in Paris along with a bout of cramp.
"The shoulder is not great, but that wasn't the issue today. I got a bit sick last night, didn't really sleep. That's just a reality," said Auger-Aliassime, who reached the fourth round at Roland Garros last year.
"I woke up this morning trying - I mean, it's like I've been struggling with a few things, and can you believe it, I get sick the day before my match?
"I tried to warm up. I tried to see the doctor, see what I could take, but after one set, just cramping and just can't move anymore.
"I wasn't sure whether I should keep going or give myself a shot or if I should stop. It was a difficult time but it's okay. I just need to get healthy again."
Auger-Aliassime said he was hopeful of returning to action during the grasscourt swing after a break.
"I hope that will help and I can play on grass in two or three weeks, but it's difficult to say," the Canadian added.
"I think I must go home, take some tests because I didn't have time to do specific tests. I have to do a battery of tests to see why I was sick here, why I was sick a week ago and see what's happening.
"I tried everything. I tried to hang on, but next time I'm on the court I want to be in good shape."