But left-arm spinner Rangana Herath had West Indies in early trouble in their reply by dismissing openers Kraigg Brathwaite (19) and Shai Hope (23) cheaply to send the tourists to stumps on 66-2, trailing Sri Lanka by 418 runs.
Darren Bravo (15) and Marlon Samuels (seven) were unbeaten at the crease for the tourists.
Earlier, with the slow pitch offering little assistance for the bowlers, left-hander Karunaratne, unbeaten on 135 overnight, and Chandimal continued to plunder runs for the hosts who won the toss and chose to bat.
Karunaratne hit 16 fours and a six in his 354-ball knock and was finally out when he offered a return catch to part-time off-spinner Marlon Samuels.
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West Indies made life difficult for themselves by spilling chances on the opening day and they again failed to make most of their opportunities on the second morning.
Chandimal, who was dropped on 11, survived another chance on 82 when Jermaine Blackwood allowed the ball to burst through his fingers at point off fast bowler Shannon Gabriel.
Right-handed batsman Chandimal made the most of his luck and completed his fifth hundred in tests with a lofted drive over mid-off against Gabriel.
He hit 16 fours and two sixes in his stroke-filled 298-ball knock before falling for 151 to paceman Jerome Taylor.
West Indies got their second breakthrough of the afternoon session when debutant Milinda Siriwardana (one) edged Taylor to wicketkeeper Denesh Ramdin.
Sri Lanka captain Angelo Mathews (48) fell to his West Indies counterpart Jason Holder with the first ball after the tea break before Bishoo got in on the act.
He took three of the remaining four wickets to polish off the tail.
(Reporting by Sudipto Ganguly in Mumbai; Editing by Nick Said)
