Gill has gone 18 innings in T20 Internationals without a 50 and missed Friday's match against South Africa with a foot injury.
Sanju Samson has impressed in the limited opportunities and made a breezy 37 as Abhishek Sharma's opening partner, replacing Gill in Ahmedabad.
Kishan was recalled after the wicketkeeper-batsman led Jharkhand's successful campaign in the Syed Mushtaq Ali Trophy, smashing a hundred in Friday's final against Haryana.
The same squad will play a five-match home T20 series against New Zealand next month.
"It's more to do with the combination that we want to play, or what the team management is comfortable with playing," chief selector Ajit Agarkar told reporters in Mumbai.
"We felt the keeper at the top at this point gives us a lot more solidity than anywhere else in the team to play different combinations.
"There are only 15 that we could have picked. Someone has to miss out. It's him. It's not because he's not a good player."
Jasprit Bumrah will lead India's pace attack, which also contains left-arm seamer Arshdeep Singh.
Varun Chakaravarthy will spearhead the spin department, which also includes left-arm wrist-spinner Kuldeep Yadav.
India will also expect Hardik Pandya, their premier seam-bowling all-rounder, to play a crucial role in their title defence in the tournament to be played between February 7 to March 8 across eight venues in India and Sri Lanka.
India squad: Suryakumar Yadav (captain), Abhishek Sharma, Sanju Samson (wicketkeeper), Tilak Varma, Hardik Pandya, Shivam Dube, Axar Patel (vice captain), Rinku Singh, Jasprit Bumrah, Harshit Rana, Arshdeep Singh, Kuldeep Yadav, Varun Chakaravarthy, Washington Sundar, Ishan Kishan (wicketkeeper)