The second Test will get underway on March 12 in Bangalore.
Karunaratne further said that Chameera's workload was being managed keeping in mind the T20 World Cup, slated to be held in Australia later this year.
"The [Sri Lanka team] medical panel has told us that we have to manage his injury till the T20 World Cup, and that he should be used (only) for white-ball cricket," ESPNcricinfo quoted Karunaratne as saying.
Earlier, the Sri Lankan captain had hoped to have Chameera in his side for the second Test, having rested him from the series opener. Chameera had featured in all eight T20Is Sri Lanka have played since on the tour of Australia and India. He is considered a vital cog in Sri Lanka’s bowling attack for the upcoming T20 World Cup.
Nissanka's absence would also hurt the visitors in the Day-Night Test. He was the top scorer in Sri Lanka’s first innings in Mohali with 61 not out.
Having lost the first Test by an innings and 222 runs, Sri Lanka have already conceded a 1-0 lead to India in the two-Test series.
(With ESPNcricinfo inputs)