The AL East champion Yankees close the regular season on Wednesday night at Tampa Bay, which could be an important game for the Rays in the AL wild-card race.
"It puts me in a pickle," Girardi said before Monday night's series opener. "I'm trying to win every game. I'm making moves to win games, but I'm not jeopardizing my guys."
Tampa Bay started play Monday one game behind Boston for the final AL postseason spot.
New York has already clinched home-field advantage throughout the AL playoffs, which are scheduled to start Friday.
Girardi has not named a starting pitcher for Wednesday night's finale. It is possible the Yankees could use several relievers.
"My focus is to make sure our guys are ready," Girardi said.