The first T20I of five will be played in Visakhapatnam on Thursday.
Warner was the leading run-scorer for Australia in their successful CWC campaign and will now join other multiformat players who will skip the five-match series ahead of the home summer which starts with the first Test against Pakistan on December 14.
Pat Cummins, Josh Hazlewood and Mitchell Starc are also heading home along with allrounders Cameron Green and Mitchell Marsh.
“Selectors decided Warner would return home on the back of a successful yet demanding World Cup campaign,” Cricket Australia said in a statement.
The upcoming Pakistan series will be the final stage of his Test career with him having earmarked the SCG in early January for his retirement from the format.
In his place, Australia has called up all-rounder Aaron Hardie, who had made his international debut earlier this year against South Africa. Also called up was pacer Kane Richardson as Spencer Johnson suffered from a hamstring injury.
Matthew Wade will be captaining the Australian T20I team against India. There will also be a stand-in coach for the series with Andre Borovec taking charge as Andrew McDonald returns home ahead of the summer.
Updated Australia T20I squad:
Matthew Wade (capt), Travis Head, Steven Smith, Glenn Maxwell, Matt Short, Marcus Stoinis, Tim David, Josh Inglis, Aaron Hardie, Jason Behrendorff, Sean Abbott, Nathan Ellis, Kane Richardson, Adam Zampa, Tanveer Sangha