Molina was checked out by team doctors and all signs and symptoms were said to be normal.
"When he initially got hit, he kinda went back to his haunches a bit," Rays manager Joe Maddon said after the game. "He came out and just was not 100 percent right. I was not comfortable sending him back out there."
Stephen Vogt replaced Molina behind the plate.
Molina wasn't the only Rays player hurt in the weekend series. In Saturday's 5-2 win over the Braves, infielder Jeff Keppinger while sitting in the dugout was struck in the leg by a foul ball hit by Martin Prado. Maddon added Keppinger was being "checked on" Sunday by the training staff.
Bill Chastain is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.