The move, announced Friday, is retroactive to Wednesday.
Gyorko has struggled after signing a $35 million, six-year contract extension in April. He's hitting just .162.
Manager Bud Black said Gyorko had an anti-inflammatory shot, will use a walking boot and will wear a strap when he sleeps to keep the arch stretched out.
Taking Gyorko's roster spot is left-hander Eric Stults, who was activated from the bereavement list. He's scheduled to start Sunday against Washington.
The Padres will make two more roster moves Saturday, when right-hander Andrew Cashner is due to be activated from the disabled list. He has been out with a sore elbow. Cashner is scheduled to start that night.