X-rays did not reveal a break. A team spokesman said Bailey would be evaluated Thursday.
Bailey allowed singles to all three batters he faced. Two runs scored on Pujols' single when Bailey's late throw to first was wild.
The right-hander left the field after a brief meeting with manager Dusty Baker and trainer Mark Mann.
Carlos Fisher replaced Bailey, who entered 0-3 with a 6.04 ERA in his last four starts.