Smyly was throwing simulated games against Cubs hitters in July and hoped to go on a rehab assignment in the minors by Aug. 1. But his recovery hit some snags, and he never made the rehab starts.
"We felt it was more important to end his season to get him the right amount of rest moving forward, so we took it out of his hands," said Cubs president of baseball operations Theo Epstein. "He felt strongly about wanting to push through and contribute."
Smyly was signed to a two-year, $10 million deal in the offseason with the expectation that he would be fully recovered in 2019 and the hope that he might be able to come back late this season to help in the stretch run.
ESPN's Jesse Rogers contributed to this report.