Manager Jim Riggleman opted to put Willie Harris in center field and the leadoff spot, giving Morgan an extra day of rest before the team travels to Milwaukee for a four-game series against the Brewers beginning Monday.
Morgan said the injury was nothing serious.
"I just lost water over the last few days and just dehydrated and pulled it a little bit," he said.
With Saturday's game ending past midnight, and the Nationals playing an afternoon game on Sunday, Riggleman did not want to test Morgan with a short turnaround.
"[Friday] when I gave him a day off," Riggleman said, "after I posted the lineup he mentioned, 'That's probably a good thing, because I've got a little tightness in my hamstring.'
"Yesterday, I made the lineup with him in there, and he was fine. Last night I checked with him after the game and he said, 'I'm all right, but I kind of feel something there.' After the short turnaround today, we're gonna hopefully get him back 100 percent tomorrow."
Morgan has been a spark for the Nationals both offensively and defensively since being traded from Pittsburgh in June. In 20 games with the Nationals, he his batting .372 with 11 stolen bases.
Mark Selig is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.