Mashrafe picked up the injury during a training session shortly after he attended Bangladesh team’s formal press conference in Mirpur ahead of the tour.
Left-arm spinner Taijul Islam and top-order batsman Anamul Haque were also recalled to replace Shakib and batsman Liton Das, who has been rested for personal reasons.
Bangladesh dropped down to eighth place at the end of the league phase of the World Cup after South Africa defeated Australia
'I'll go home and rethink': Bangladesh captain Mashrafe Mortaza coy over future after World Cup exit
Asked how he rated Bangladesh's campaign, Mashrafe conceded they had been exposed at times in their sloppy fielding, while his bowlers found it hard to thrive in English conditions.
Mashrafe's side have seven points after three wins and a washout, three points behind fourth-placed England.
Rezaul Karim, a child cancer specialist, was posted to the southeastern district of Rangamati weeks after criticising skipper Mashrafe Mortaza on Facebook.
Bangladesh's skipper Mortaza who became a member of the Bangladesh parliament earlier this year has never talked about his retirement plans before.
Jason Roy's 153 took the hosts to an imposing 386 for six, leaving Bangladesh needing to surpass Ireland's total of 329-7 against England in 2011, to win.
Mushfiqur took the ball in front of the stumps, with his feet behind, and tried to break the stumps.
Bangladesh started their World Cup campaign on a perfect note, posting their highest one-day international score of 330 on the back of half-centuries by Shakib Al Hasan (75) and Mushifiqur Rahim (78).
The number one ODI all-rounder had a rather off day with both bat and ball in their warm-up game against India which Bangladesh lost by 95 runs on Tuesday.
Supporters were jubilant after a tri-nation series win against Ireland and West Indies on the weekend handed Bangladesh its first ever multi-team tournament trophy.
Mashrafe Mortaza's arrive in England confident of making the last four on the back of impressive form that marks them as a serious threat to the established order.
There were questions raised over MS Dhoni's batting form, but in the last few months, the 37-year old has shown his finishing abilities are just where they should be.
West Indies, for whom Shai Hope made 109, were well-placed at 205 for two in the 41st over before slumping to 261 for nine in 50 overs, with pace-bowling captain Mortaza taking three for 49.