Harmison, 29, left the field with a back spasm just three balls into a fourth spell of the day at the Nondescripts Cricket Club.
Fellow paceman James Anderson finished the over, after Harmison departed, holding the problem area, alongside physio Kirk Russell.
Harmison earlier claimed the wicket of home captain Tillekaratne Dilshan and had figures of 10.3-1-45-1 when his injury jinx struck again in the 62nd over.
England's management opted to give Harmison a chance to prove himself in this match - omitting Stuart Broad in the process - ahead of the first Test in Kandy, which begins next Saturday.
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