Flaherty was out from April 23 to May 8 with a right groin strain. He aggravated the injury on Monday night in the third inning against Toronto and was removed from the game.
Flaherty is batting .250 with three doubles and two RBIs in 13 games.
To fill out the infield, Baltimore recalled Rey Navarro from Triple-A Norfolk. The 25-year-old made his major league debut with Baltimore on April 24 and was sent to the minors when Flaherty was activated from the DL on Friday.
Navarro went 6 for 19 with two doubles in seven games with the Orioles.