Australia defeated the hosts by six wickets in front of nearly 100,000 in Ahmedabad on Sunday to clinch their sixth one-day World Cup crown.
The two countries meet again in a five-match T20 series starting on Thursday in Visakhapatnam, but the 37-year-old Warner will not stay on after all.
His withdrawal means just seven of Australia's World Cup-winning one-day squad will remain in India for the series, among them Travis Head, Glenn Maxwell and Steve Smith.
All-rounder Aaron Hardie replaces Warner, who is gearing up to say farewell to Test cricket.
"Selectors decided Warner would return home on the back of a successful yet demanding World Cup campaign," Cricket Australia said in a statement.
Warner was Australia's leading scorer at the World Cup with 535 runs at 48.63.
For the hosts, Suryakumar Yadav will captain India for the first time in the absence of regular skipper Rohit Sharma.
Just three of India's World Cup squad will remain for the T20 series.
The open match in Visakhapatnam is followed by games in Thiruvananthapuram on November 26 and Guwahati on November 28.
Shreyas Iyer will join the squad as vice-captain for the last two T20s, in Raipur on December 1 and in Bengaluru on December 5, the Board of Control for Cricket in India (BCCI) said.
India squad: Suryakumar Yadav (Capt), Ruturaj Gaikwad (vice-captain), Ishan Kishan, Yashasvi Jaiswal, Tilak Varma, Rinku Singh, Jitesh Sharma (wk), Washington Sundar, Axar Patel, Shivam Dube, Ravi Bishnoi, Arshdeep Singh, Prasidh Krishna, Avesh Khan, Mukesh Kumar.
Australia squad: Matthew Wade (Capt), Aaron Hardie, Jason Behrendorff, Sean Abbott, Tim David, Nathan Ellis, Travis Head, Josh Inglis, Glenn Maxwell, Tanveer Sangha, Matt Short, Steve Smith, Marcus Stoinis, Kane Richardson, Adam Zampa.
