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 then 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 in the fifth.
Prado, an All-Star, was hitting .307 with 15 home runs and 66 RBIs entering the game. He was replaced by Brooks Conrad.