Pitching in relief of starter Darrell Rasner, Giese opened the sixth inning by allowing a leadoff single to Joe Mauer before walking both Justin Morneau and Jason Kubel. He then left the field with assistant trainer Steve Donohue.
"The shoulder just stiffened up on me while I was trying to face Mauer," Giese said. "I was trying to overthrow. It just got progressively worse and worse, the more pitches I threw."
Yankees manager Joe Girardi said that Giese's scheduled start for Tuesday at Toronto will not be affected by the injury, but Yankees spokesman Jason Zillo said that Giese is scheduled to be examined by Dr. Chris Ahmad on Thursday at New York Presbyterian Hospital.
"He's OK, he's just a little stiff," Girardi said. "We just thought it was best to get him out. He didn't feel it warming up. ... It shouldn't jeopardize Tuesday."
Giese, who is 1-3 with a 2.58 ERA in 15 games (three starts), compared the sensation to the aching of a tetanus shot or being punched deeply in the meaty part of the shoulder.
"I've had it in the past," Giese said. "If you give it some time to progress, usually it bounces back pretty well. I'm hoping that's what happens."
David Robertson relieved Giese and was provided as much time as necessary to warm up.
Giese, a 31-year-old rookie, started on Saturday at Anaheim and limited the Angels to one run over six innings, throwing 83 pitches. He was to have his start skipped this week because of the Yankees' off-day on Thursday, and he said that he did not believe coming back on short rest had affected him.
"You never know," Giese said. "I've done it before, so it wasn't anything new for me. I don't think that played into it."
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.