Flaherty threw 49 pitches, allowing one hit, walking two and striking out two before being relieved by right-hander Nick Wittgren in the top of the third inning. The Cubs won Sunday's game 6-5 in 10 innings.
Flaherty was not available after game. Cardinals manager Oliver Marmol said Flaherty had a, "dead arm sensation.''
Flaherty, 26, didn't make his debut this season until June 15 because of an ailment in his right shoulder. He had a platelet-rich-plasma injection in his shoulder in early March to treat inflammation.
Marmol said Sunday's ailment was not connected to Flaherty's previous injury.
This was his third start since returning. He was 0-0 with a 7.50 ERA entering Sunday's start.
He was 9-2 with a 3.22 ERA in 17 starts last season when he was slowed by an oblique injury.
The Associated Press contributed to this report.