Flaherty will take the roster spot of Adam Wainwright, who was placed on the 10-day disabled list retroactive to May 14 with an injury to his right elbow that forced him out Sunday's game at San Diego.
He told reporters he felt discomfort in his elbow during pre-game warmups, but attempted to pitch through the pain.
He walked six and allowed two runs on three hits in the eventual Cardinals loss.
The 23-year-old righty made a second rehab appearance Monday night, throwing five scoreless innings at Single-A Peoria.
His return to the majors is likely imminent, which means the Cardinals will have to make tough decisions as to where he fits and what that means for the aging and ailing Wainwright.
The team has called up pitcher Jack Flaherty from Triple-A to replace Wainwright in the rotation. Flaherty is set to start in the series opener against the Minnesota Twins.