The 35-year-old was 2 under after 36 holes, 11 shots back of leader Hunter Mahan.
"Not real sure how to describe the emotions of withdrawing this AM from @RBCCanadianOpen," Fritsch posted on his official Twitter account. "Just can't handle the back pain."
Fritsch shot 69 on Thursday and was on his way to another good round on Friday before bogeying two of his final four holes to finish with a 73.
It's unclear when Fritsch, who is in his first season on the PGA Tour, suffered the injury.