Malinga flew home on Friday. A replacement was yet to be named.Sri Lanka gambled with an unfit Malinga in hope the pace bowler would improve in their bid to defend the title.
He bowled with a shorter run-up during practices since the team arrived in India, but sat out the team's victory against Afghanistan in Kolkata on Thursday.
He was injured during the Asia Cup, and handed over the captaincy to Angelo Mathews.
Malinga, who has taken 38 wickets in 31 World T20 matches, was key to helping Sri Lanka reach three of the last four World Twenty20 finals.
Knee injury puts Osaka's US Open title defense in doubt