The Orioles are already without second baseman Jonathan Schoop, out since April 18 with a right knee sprain, and shortstop J.J. Hardy, who hasn't played this season because of a strained left shoulder.
Flaherty, who's batting .300 with two home runs and four RBIs, suffered the injury running to second base on the final play Wednesday.
Manager Buck Showalter said Flaherty could go on the disabled list if he doesn't improve before the Orioles open a three-game series at home to Boston on Friday.
Showalter spoke to general manager Dan Duquette about options to replace Flaherty before Thursday's game.
Jimmy Paredes made his first start of the season at second base Thursday.