Surrey's 19-year-old all-rounder Sam Curran along with England fast bowler Tymal Mills have also been added to the World XI squad.
"I have a small fracture in the ring finger of my right hand", Morgan explained.
"It's a great honour to be leading the ICC World XI side, that too for such a good cause". This match will also see Afridi make a return to global cricket on a one-off basis having last played for Pakistan in the World T20 in 2016.
While the injury is not serious, Morgan is set to be out of action for a week.
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Sam Billings will deputise for wicketkeeper Jos Buttler for the Scotland clash, with seamer Tom Curran bolstering the ranks for the Australia series.
Eoin Morgan expects to recover from a fractured finger in time to lead England in their first limited-overs assignment of the summer.
England then host Australia in a five-match series starting on 13 June. Morgan had been due to captain an ICC World XI against West Indies in a T20 match at Lord's tomorrow to raise money for cricket grounds in Dominica and Anguilla that were destroyed by hurricanes past year.
Other names in the World XI squad include Rashid Khan, Adil Rashid and India wicket-keeper Dinesh Karthik. "It is not a huge concern, it is one we can hopefully manage past in about a week", Andy Flower, who is standing in as England's director of cricket for Andrew Strauss, was quoted as saying by the International Cricket Council (ICC) website.