Thilan Thushara will replace Murali, who has been struggling with a groin problem, after the International Cricket Council (ICC) gave Sri Lanka permission to summon the left-arm pace bowler.
Tournament rules state that once replaced, a player cannot return so Saturday's announcement means the World Twenty is over for Murali.
He suffered the injury during Sri Lanka's tournament-opening loss to New Zealand in Guyana and missed the subsequent victory over Zimbabwe, where his place was taken by fellow off-break bowler Suraj Randiv.
But Murali played in Sri Lanka's 57-run Super Eights win over the West Indies at the Kensington Oval here on Saturday.
Afterwards, Sri Lanka coach Trevor Bayliss said Murali "didn't look great".
The 29-year-old Thushara has represented Sri Lanka in nine Tests, 36 one-day internationals and five Twenty20 Internationals.
His last Twenty20 international was against Pakistan in August 2009.
Sri Lanka's next Super Eights match is against Australia on Sund