Jeter was a late scratch from New York's lineup after he sustained a right knee contusion on a foul ball in the first game of the twin bill, and Rodriguez is again being bothered by his sprained left thumb.
"We need to get them healthy," Yankees manager Joe Girardi said. "It is somewhat of a concern, but hopefully neither one of them will be out very long. I don't know if we'll have either one of them [Monday]."
Jeter fouled a ball off the top of his right kneecap in the third inning against Baltimore's Zach Britton, but stayed in the game, going 0-for-4 in New York's 2-0 loss.
The captain said between games that he expected to play, but was taken out of the lineup minutes before first pitch due to swelling. X-rays on the knee were negative, and he is day-to-day.
"We'll see what happens," Jeter said. "You guys asked me between games, and I told you I was fine. I really was fine. It's really bizarre, to be quite honest with you. After we iced it was when it swelled up."
Rodriguez went hitless in four at-bats in Game 1 and was unavailable, Girardi said, due to discomfort in his left thumb. Rodriguez originally sprained the thumb last Sunday in Minnesota backhanding a Joe Mauer infield single.
"His thumb is bothering him, so we just felt it wasn't in our best interests to play him either," Girardi said.
Eduardo Nunez replaced Jeter at shortstop and Eric Chavez filled in at third base.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.