He will be limited to 60 pitches.
Cardinals manager Oliver Marmol made the surprise announcement before the first game of a day-night doubleheader against the Pirates on Tuesday. Flaherty had been scheduled to make his third rehab start at Triple-A Memphis on Wednesday.
Flaherty has been sidelined this season by a right shoulder ailment. He had a platelet-rich-plasma injection in his shoulder in early March to combat inflammation.
He has made two rehab appearances, pitching seven innings, allowing one run and one hit (a home run) and striking out nine batters.
He was 9-2 with a 3.22 ERA in 17 starts last season when he was slowed by an oblique injury.
Flaherty, 26, is 32-24 with a 3.34 ERA in five major league seasons.
The Associated Press contributed to this report.