Murphy was pulled in the sixth inning due to discomfort in his right side. The Indians are trying to schedule an MRI exam for Sunday morning to determine the extent of the injury. Swisher was replaced in the seventh after his troublesome right knee flared up on him once again.
"We're going to have to figure some things out here," said Indians manager Terry Francona.
Francona would not speculate about whether either player was bound for the disabled list, but it is a safe bet that neither will see the field in Sunday's finale at Yankee Stadium. With a scheduled off-day looming on Monday, Cleveland might also have the ability to delay a trip to the DL for one or both of the players.
Cleveland is currently without center fielder Michael Bourn, who is in the midst of a Minor League rehab assignment with Double-A Akron. While Bourn has been sidelined for the past month, Michael Brantley has handled the duties in center. On Friday and Saturday, though, Brantley served as the designated hitter due to general soreness in his legs.
Murphy, who has hit .262 with seven home runs and 55 RBIs in 109 games this season, said his right side has been sore for the past week, but he tried to play through the mild discomfort. In the fifth inning on Saturday, Murphy struck out swinging and experienced a heightened level of pain in his oblique area.
"It grabbed at me a little bit more, my right side, than it has been," Murphy said. "I don't feel like it blew out, but I feel like it got to the point where it was close enough to where I didn't want to test it any more."
Swisher has dealt with knee issues off and on this season, contributing to a poor offensive season that has included a .207 average and .277 on-base percentage through 96 games. Over the past few games, Swisher has manned both left and right field, following an extended period as Cleveland's primary DH.