The left-hander pointed to his forearm when visited by manager Clint Hurdle and a Pirates trainer in the first inning Wednesday. After a brief discussion on the mound, Rodriguez was removed from the game.
Rodriguez gave up two hits and a run and hit Braves first baseman Freddie Freeman with his 14th and final pitch.
Bryan Morris replaced Rodriguez.
The Pirates had no immediate word on the severity of the injury.
At 6-3 with a 3.47 ERA, Rodriguez is one of Pittsburgh's top starters. He left a game April 8 at Arizona with a left hamstring strain and missed one start.
The Pirates were 8-3 in Rodriguez's first 11 starts.