Jeter was set to bat leadoff for Friday night's game at the Texas Rangers after missing one game with a stiff hip.
Chavez broke his left foot Thursday in the game that Jeter missed and was put on the 15-day disabled list. Chavez, who is hitting .303 in 17 games for New York, got hurt running the bases in the fourth inning of the loss in Detroit.
"He's going to be in a boot for two weeks and then they'll make an evaluation after that, to see if it's healing," manager Joe Girardi said. "It happened somewhere between second and third. I don't know if it happened on the step he hit the bag or the next step, but that's right in the area that it happened. It's strange, it's unfortunate."
Jeter missed the game after leaving late in Wednesday night's game with a right hip problem. Girardi described it then as day to day, and Jeter said it was nothing serious.
"He said he just felt like his hip caught, like it just needed it to pop. [Thursday] he felt better, he said he felt fine, and today he's fine, so I put him back out there," Girardi said before the Yankees' first game in Texas since the AL championship series last October. "We didn't necessarily have an injury, but he just said it was stiff."
While Jeter was back, Nick Swisher was scratched from the original lineup Friday because of illness. Swisher has been dealing with a head cold for several days, though he hasn't had any fever.
"He'd been sick, but today it's the worst he's been," Girardi said. "You play in this heat and it runs you down more. It's something that could linger. He didn't sleep much last night, so I decided to give him the day."
The Yankees recalled infielder Ramiro Pena from Triple-A Scranton/Wilkes-Barre, where he hit .233 in 24 games.