Gunaratne sustained the injury while fielding at second slip. He hurt his thumb while attempting a catch of India opener Shikhar Dhawan off the bowling of Lahiru Kumara.
Dhawan was batting on 31 when Gunaratne put down the chance. The India opener later went on to register his fourth Test half-century just before lunch.
Such was the severity of the injury that Gunaratne has been rushed to Colombo for an operation. Gunaratne's injury means Sri Lanka will bat with only 10 players in both their innings.