Prado swung at a 1-1 pitch with runners at first and third and two outs, and hit it back to Florida right-hander Alex Sanabia.
Prado grabbed his left side and grimaced after taking one step from the batter's box. Manager Bobby Cox and assistant trainer Jim Lovell helped him to the dugout.
He was diagnosed with a left hip pointer and was listed day to day. He said he originally injured himself on a diving catch in the fourth inning, then aggravated it when he swung the next inning.
Prado said he took two pain pills, iced down three times. He indicated he was day to day although he admitted when he swung he "heard a pop and couldn't run."
Cox said he would "definitely be out a while."
Prado, an All-Star, is hitting .307 with 15 home runs and 66 RBIs entering the game. He was replaced by Brooks Conrad.
"With five games left anytime you lose a guy like Prado it's not good. Guys will just have to step up," said Brian McCann, who hit a solo home run in the game. "Conrad can do it. He's done it before."