Pineda had to cut his outing short after just 15 pitches and will be sent to see a physician in Tampa, Fla., on Monday, Yankees manager Joe Girardi said.
"I think it's somewhat significant, just because you were expecting him to build up," Girardi said. "Now, you're going to have to give him probably a little bit more time than we did before. I can't tell you when we'll get him back now."
The 23-year-old Pineda fell out of a Spring Training rotation competition when he was diagnosed with shoulder tendinitis after a March 30 Grapefruit League start.
Saturday marked Pineda's first time throwing in a game situation after rebuilding strength by working out and long-tossing at the Yankees' complex in Tampa.
"The one thing that you can't control is when the intensity turns up, how a guy is going to feel," Girardi said. "He still felt it."
Pineda was acquired from the Mariners in a blockbuster January deal along with Minor League right-hander Jose Campos in exchange for catcher/designated hitter Jesus Montero and right-hander Hector Noesi.