Green sustained the injury during training and will undergo a short rehabilitation period. While not serious, Cricket Australia is taking a cautious approach ahead of the Ashes, which begin in six weeks.
Green is expected to return for Western Australia's next Sheffield Shield match starting October 28.
The 26-year-old all-rounder had only recently resumed bowling following back surgery and was managing restricted workloads. He was already set to miss the third ODI and the T20I series to focus on red-ball preparations.
Labuschagne, who was initially left out of the squad, has earned a recall after scoring four centuries in five domestic innings, including two in the One-Day Cup. He will join the squad in Perth after completing Queensland's current Sheffield Shield match.
Australia are already without several first-choice players, including Pat Cummins, Josh Inglis, and Adam Zampa, for at least part of the India series, which begins Sunday in Perth.