According to a statement released by Sri Lanka Cricket, the 32-year-old sustained an arm injury while fielding in a practice session ahead of the first game in Dhaka which he missed.
Gunaratne will undergo a scan in Sri Lanka and will miss the second game in Sylhet which will be played on Sunday.
This is Gunaratne's second injury recently after he suffered a fractured left thumb during the Test series in India and was sidelined for almost five months.
Sri Lanka have already lost the services of opener Kusal Perera and captain Angelo Mathews after they suffered a side-strain and a hamstring injury respectively during the recently concluded One-Day International tri-series.
Sri Lanka currently have taken a 1-0 unassailable lead in the two-match series following their six wicket victory chasing 194 in the first game in Dhaka.
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