Jeter was hit on the left elbow by Kris Benson's pitch to start the sixth inning. The Yankees captain stayed in the game to run the bases before being replaced at shortstop by Rey Sanchez in the bottom half.
"It swelled up pretty quick and hurt a bit," said Jeter, who added he plans to play Sunday. X-rays on his elbow were negative.
Beltran could be out longer. He departed after the fifth because of a strained right quadriceps and was replaced in center field by Mike Cameron, who moved over from right. Left fielder Cliff Floyd took Beltran's No. 3 spot in the Mets' lineup, and Chris Woodward shifted from left to right.
Beltran felt the injury running from first to third in the first inning, and the pain got worse when he tracked down Randy Johnson's flyball to end the fifth.
"I just told Willie [manager Randolph], 'Willie, take me out because I'm not going to be able to play 100 percent,'" Beltran said. "It's been bothering me for maybe two weeks, but not like today. Today I feel pain."
Also, Mets second baseman Kaz Matsui came out in the sixth with a strained upper back. The Mets said he and Beltran were day-to-day, and Beltran added he will be the one to decide when he returns.