Hales fractured his right hand while attempting a catch during the second ODI in Cuttack on Thursday (January 19), ruling himself out of the third ODI as well as the T20 series.
His replacement, Bairstow, was already part of the ODI squad and will now remain in India till the end of the tour. (3rd Ind-Eng ODI preview)
The England team announced the inclusion of Bairstow in the T20 squad on its Twitter handle.
While Bairstow is yet to feature in the ODI series, he kept wickets for all five Test matches that preceded the limited overs series. After Tests, England face another whitewash in the ODI after trailing 2-0.