Prado hasn't played since he tumbled crossing first base Sunday against Colorado and landed hard on his shoulder. The move made Thursday is retroactive to June 15.
Marlins manager Dan Jennings said the decision was made because Miami didn't want to go into its series at Cincinnati with a short bench.
The Marlins selected the contract of catcher Jhonatan Solano from Triple-A New Orleans to fill Prado's spot.
Miami needed a catcher because starter J.T. Realmuto has been out with back tightness.
Jennings said Realmuto could be used in an emergency Thursday night against the Yankees but he doesn't want to risk further injury.