After a visit with the team trainer, Amarista was replaced with pinch-runner Christian Bethancourt.
Padres manager Andy Green said after the game that Amarista was sore, but the team wasn't sure if the injury would require a DL stint at this point.
"We'll wait and see where he is tomorrow," Green said. "I wouldn't want to handicap it right now."
With one hit in three at-bats Monday, Amarista was hitting .389 (7-for-18) through seven games in July and August.
"It's frustrating," Green said. "He's been through so much and he's been playing so well too. Tons of energy, good at-bats since he's been back with us… He really was playing himself into a consistent opportunity.
"I know it's frustrating for him, it's kind of frustrating for all of us. We've gone through this all season long."
Carlos Collazo is a reporter for MLB.com based in San Diego. Follow him on Twitter @CarlosACollazo. This story was not subject to the approval of Major League Baseball or its clubs.