Pradeep, who had taken six wickets in the opening Test, could be out for a couple of months.
"Nuwan Pradeep's out for one or two months," Sri Lankan opener Dimuth Karunaratne said at the press-conference.
With Pradeep ruled out, Karunaratne, who took 1-31 in the first innings, will have to bowl his gentle medium pace if there is a second India innings.
"I started my career as a bowler, not as a batsman, so I can bowl. The thing is there are a lot of bowlers who can bowl faster than 130-135," he said.
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Pradeep could bowl only 17 overs on the opening day. He had left the field complaining of a hamstring niggle and it was confirmed today that he would not bowl for the rest of the Test but will bat.
Sri Lanka is already going through a tough phase due to injuries to their key players. All-rounder Asela Gunaratne was ruled out of the three-match series after he broke his thumb in the Galle Test.
India had defeated Sri Lanka by 304 runs in the first Test.