The 29-year-old Souza reinjured the pectoral muscle on a throw from right field on Friday night. He originally hurt it during spring training and didn't start his big league season until May 3.
Outfielder Socrates Brito was recalled on Tuesday from Triple-A Reno to replace Souza.
An MRI on Saturday determined Souza suffered a strain and had inflammation.
"Obviously, a little more sore than I'd like,'' he said.
Diamondbacks manager Torey Lovullo initially described the injury as inflammation; after being told Souza called it a strain, Lovullo confirmed the strain diagnosis. Lovullo said Souza slipped chasing a ball down the line earlier in the week, and that started to cause the tightness.
In his first season with Arizona, the former Tampa Bay Rays player is hitting .167 (7-for-42) with one RBIs.