The Yankees captain, 0 for 9 in four games, hit into his third double play in the first and had a grounder to third during the third.
Jeter, who announced last month that he will be retiring after the 2014 season, broke his left ankle in the 2012 AL championship series and was limited to 17 games last year.
Jeter was the designated hitter Tuesday in his first back-to-back games this spring. He played shortstop in in a 4-2 win Monday over the Washington Nationals.
Jeter had already left the clubhouse before it was opened to reporters late in the game.
"I just feel comfortable right now," Chen said through an interpreter.
Yankees: Fifth starter candidate David Phelps, who worked out of two-on, no-out jams in the first and second, gave up one run and five hits in 2 2/3 innings.
Orioles: Right-hander Edgmer Escalona has been shut down for three weeks due to right shoulder inflammation.
Outfielder Henry Urrutia (right shoulder) could return in a few days.
Yankees: Manager Joe Girardi remains optimistic that first baseman Mark Teixeira (wrist) and outfielder/designated hitter Alfonso Soriano (flu-like symptoms) will both play in their first spring training game Thursday against Philadelphia.
Shortstop Brendan Ryan played with a bruised left hand. He got hit by a liner during batting practice.
Yankees second baseman Brian Roberts admitted it was a "little different" facing his old team for the first time.
Roberts, signed by New York as a free agent, played for the Orioles from 2001-13.
"It's part of the business," Roberts said. "I think they decided to go in another direction."
The 36-year old Roberts hasn't appeared in more than 77 games the past four seasons due to injuries.
"I hope he's healthy for his sake, but not for the Yankees' sake," Baltimore manager Buck Showalter said. "I think he will be, too. It's all about timing sometimes. He'll do every bit of work it takes to be on the field. That's never been a question."
Roberts, who broke the window of Yankees co-chairman Hank Steinbrenner's office with a foul ball, went 1 for 1 with a walk.
"You try to be as fair as you can to everyone on the club because you know that you need at least 25 guys, and usually need more during the course of the season," Girardi said. "Just talk to him, this is what we're thinking. I have a ton of respect for what he's done and what he does now. I can't tell you what the breakdown is going to be, but all these guys are important to us."