“Kasun Rajitha will not be available for the second Test match as the player has sustained an injury to the left upper back area,” Sri Lanka Cricket said.
Fernando last took 10 wickets while playing a Test match in Bangladesh in 2022.
He last played a Test against Afghanistan in February.
He was initially ruled out of the Bangladesh series with a hamstring injury, but was reinstated into the squad for the second Test.
Sri Lanka has never lost a Test series to Bangladesh.