Last week, Malinga had left the Bangladesh Premier League (BPL) early due to personal reasons, despite his team Rangpur Riders playing the final.
Senior players Suranga Lakmal and Lahiru Thirimanne have also been rested while Vishwa Fernando and Dasun Shanaka have replaced them in the squad.
The first match will be played at Cuttack on December 20 followed by matches in Indore and Mumbai on December 22 and 24 respectively.
Sri Lanka T20I Squad: Thisara Perera (Captain), Upul Tharanga, Angelo Mathews, Kusal Janith Perera, Danushka Gunathilaka, Niroshan Dickwella (WK), Asela Gunaratne, Sadeera Samarawickrama, Dasun Shanaka, Chaturanga de Silva, Sachith Pathirana, Dananjaya De Silva, Nuwan Pradeep, Vishwa Fernando, Dusmantha Chameera.
