The Braves right-hander allowed four runs and seven hits in a season-low four innings. He also gave up his first two home runs of the season.
Smoltz (3-2) came in having allowed just two runs in his first four starts, for a 0.78 ERA.
Smoltz said the discomfort prevented him from delivering pitches the way he wanted. He was vague about what will happen next.
"The next couple of days I should know what paths we're looking at," Smoltz said.
Smoltz started the season on the disabled list with tightness in the back of the shoulder.
"He's been dominating all season," manager Bobby Cox said. "This is the only time he didn't dominate."