The setback comes on the eve of their clash against a spirited Afghanistan. Pacer Shafiul Islam has been brought as Mortaza's replacement.
There is a cloud of uncertainty over in-form skipper Mushfiqur Rahim, who scored a century in their six-wicket loss to India, as he is nursing a shoulder injury.
"Mortaza had picked up a side strain during the match against India on 26 February. The scan report suggests it is a strain on the left side. Unfortunately he is out of this tournament.
The physio also said Mushfiqur's scan report had come in and more monitoring was needed.
"We will continue to asses him today. He will undergo a fitness test tomorrow after which we will decide whether he can play the match against Afghanistan."
Bangladesh are already missing talented batsman Tamim Iqbal and Shakib-al Hasan, who was handed a three-match suspension after a lewd gesture on live TV.
Shakib's suspension, however, will end after their match against Afghanistan.
