Samardzija will have further tests on the shoulder Thursday, the team said.
Samardzija gave up two runs on three hits to the Colorado Rockies on Tuesday in one inning of work. He was so frustrated when he was pulled that he snapped a bat over his knee in the dugout.
The right-hander said he has been bothered by the shoulder for a while but had been able to work though the issue in the past couple of outings. Right-hander Tyler Beede was recalled from Triple-A Sacramento to take Samardzija's place on the roster and will be active for Wednesday night's game at Colorado.