Johnson will play in two Sheffield Shield fixtures and another match before Cricket Australia (CA) announces its squad for the Ashes series against England on November 12.
Cricket Australia's General Manager of Team Performance Pat Howard said that Johnson would return home to prepare for the longer format of the game.
"Mitch has performed very well in India, however, we believe it is best for his preparation ahead of a busy summer to have him return home to increase his bowling loads in preparation for the Ashes Test window," Howard said in a CA release.
Johnson is currently Australia's leading wicket-taker in the ODI series against India, with seven scalps in his five matches at an average of 33.42. The series is currently level at 2-2.
Johnson will leave India on Thursday and arrive in Perth on Friday.
Pacer Nathan Coulter-Nile is expected to make the playing eleven for the series decider in Bangalore.
Johnson has impressed in his limited-overs outings for Australia in England and India since he missed selection for the last Ashes series, which Alastair Cook's side won 3-0.
Australia to miss Mitchell Johnson in final ODI vs India
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