Rodriguez said he felt discomfort Thursday and the shoulder bothers him when he throws.
"Just a little bit," Rodriguez said before New York's 9-5 loss to Houston on Friday. "I certainly wouldn't miss a game during the regular season, or have to DH. But I think right now, it's just being smart."
Rodriguez, who went 1-for-2 with a double against the Astros, took part in all drills Friday except the 10-minute throwing session. At that time, he took extra grounders at third.
"I probably won't throw for a couple days," Rodriguez said. "The swing is good."
The three-time AL MVP had a heat pack on the shoulder before going through pregame drills.
Yankees catcher Jorge Posada was scratched from Friday's game due to a sore lat muscle, which he felt while throwing on Monday. Posada replaced Rodriguez as the DH in the fifth, and was hitless in three at-bats.
"Everything is fine hitting," Posada said. "I threw today and didn't feel it. I didn't push it, obviously, so it's just day to day. I'm not worried about it."
Posada could catch again next Monday.
"I told them they weren't going to play today," Girardi said. "I was going to make sure they take a couple days and make sure they're healthy."
Yankees slugger Hideki Matsui, who is coming off right knee surgery last November and missed three days of batting practice this week with neck stiffness, said he will probably play for the first time Monday or Tuesday. He will DH for a few games before possibly playing in the outfield late next week.