The pain is in the same spot where Swisher was hit by a foul ball in Toronto last week, causing him to leave one game and miss another.
He said he felt something in his knee again on Wednesday night going after a fly ball in right field. It was bothering him a bit in pregame warmups on Thursday, but he hoped to battle through it. He was pulled, however, after a first-inning groundout on which he limped out of the batter's box.
"He told me he just couldn't explode when he took off to run," manager Joe Girardi said. "He came in and iced a lot, and we'll see if he's able to go tomorrow."
Swisher was replaced in the top of the second by Curtis Granderson, who went on to hit two home runs and drive in three.
"I expected hopefully to come in later in the game, but you never know. You've got to be ready to go," said Granderson, who made a similar appearance last Saturday in Chicago replacing Mark Teixeira. "The good thing about today was I had a couple of at-bats prior to mine to get warmed up."
Swisher is hitting .295 with 25 home runs and 80 RBIs on the season.