Jeter, the Yankees shortstop and captain, batted leadoff while Matsui was in the No. 5 slot as the designated hitter.
Jeter was batting .273 with four homers and 13 RBIs. He missed the prior two games because of a sore right oblique muscle, an injury that had been bothering him for about a week, but was declared ready to return after hitting in a batting cage before the game.
Manager Joe Girardi had previously said Jeter might not play until Friday, when the Yankees return home to begin a four-game series with Minnesota. Girardi said he was a little surprised Jeter was ready Thursday.
"Seeing how he was yesterday, I wasn't convinced he would be in the lineup," Girardi said. "I was more convinced that we would get Matsui back today but [Jeter] came in and said he felt good."
Matsui, who was batting .263 with three homers and 12 RBIs, left Tuesday's game after one at-bat with a tight right hamstring and did not play Wednesday.
Girardi said right-hander Chien-Ming Wang (hip) will make a second rehab start with Triple-A Scranton/Wilkes-Barre on Sunday. Wang allowed three hits in six scoreless innings in his first rehab start on Tuesday.
"We want to see him close to what he was," Girardi said. "To me, that's consistency in his sinker and it was better last time. I'm pretty encouraged by that and I think Sunday it will be even better. At that point, we'll probably have to make a decision."
Alex Rodriguez, who has started all six games at third base since returning from hip surgery May 8, could DH Friday, Girardi said.
Left-hander Phil Coke (tight back) was not available Thursday but is expected to be ready Friday.