Having previously dealt with a similar issue earlier in the year, Shanto appeared to be in discomfort and did not return to the field for the rest of Sri Lanka's innings.
Earlier in the match, Shanto had contributed 14 runs off 19 balls before being dismissed.
He is currently resting with ice treatment, and his condition will be closely monitored over the next 24 hours.
The medical team is expected to reassess him on Sunday, with a decision on his availability for the third ODI in Kandy to follow.
