Left-hander Warnapura, opening the batting, maximised ideal conditions to give Sri Lanka a solid base, but West Indies struck back in the final period to leave the visitors on 269 for four in their first innings when stumps were drawn on the opening day.
Warnapura was caught down the leg-side, when he fenced at his short, rising 226th delivery from Dwayne Bravo about half-hour after tea to leave Sri Lanka on 205 for two.
He batted for close to 4-1/2 hours and struck 14 boundaries.
But Sri Lanka captain Mahela Jayawardene came to the wicket and kept his side on track with his deputy Kumar Sangakkara before Jerome Taylor struck twice in the space of three balls in his 16th over to drag West Indies back into the match.
Sangakkara, who was dropped on 44 at short mid-off off Taylor, flicked Test newcomer and left-arm spin bowler Sulieman Benn through backward square leg for a single to reach 50.
But he edged a loose drive in the next over from Taylor and was caught at slip without addition