Cricket Australia confirmed in a statement that the 23-year-old will head home on Tuesday, missing the fourth Test which gets under way in Delhi on Friday, and will go under the knife later this week to remove the bone spurs on his right ankle.
Australia team doctor Peter Brukner said: "Mitch has been experiencing ankle pain related to bone spurs during the India Test series and, whilst manageable, this represents an appropriate time for Mitch to have the surgery with a view to having him fully fit for the Ashes in late June."
He added: "Mitch will have surgery later this week and we'll assess his recovery as he returns to bowling."
India took an unassailable 3-0 lead in their four-Test series against Australia on Monday with a six-wicket win at Mohali, despite a first-innings knock of 99 from Starc.
Australia coach Mickey Arthur said: "We were aware that Mitch would need surgery at some point in the future to have the spurs removed.
"He could have continued playing but we want to take a proactive approach in managing Mitch to have him fit for the Ashes series in England.
"Our medical team will monitor his progress closely on whether he is available for selection for the ICC Champions Trophy."