Morgan led off the game with a sharp chopper, which was bobbled by Milwaukee shortstop J.J. Hardy, but scored a single. As he neared first base, Morgan slowed and finished his run to first with a limp.
"As soon as I was about to hit the bag, something grabbed," Morgan said afterward. "It's sore right now."
After a visit from trainer Brad Henderson and manager John Russell, Morgan left the game, though he jogged back to the dugout. The speedy outfielder confirmed afterward that he had had no problem with the hamstring before this incident.
Morgan entered the contest as one of the Pirates' most explosive offensive threats of late. He has hit .348 with 11 doubles and 20 runs scored from the leadoff spot in 31 games since being recalled from Triple-A. With the first-inning single, Morgan has reached base safely in 25 of his 27 starts since being promoted.
Jason Michaels entered the game as a pinch-runner for Morgan and remained in the game to play left field. The Pirates are already down one outfielder, with Brandon Moss shut down as he prepares to undergo surgery on his left knee next week.
Jenifer Langosch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.