The All Share Price Index closed at 3,955.83, down 0.07 percent (2.95 points) while the more liquid Milanka index fell 0.
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49 percent (22.08 points) to close at 4,520.48.
Turnover was 651 million rupees, according to stock exchange provisional figures.
The markets were closed Tuesday and Wednesday because of traditional New Year festivities which followed last week's parliamentary polls won by the ruling alliance.
John Keells Hotels was the most actively traded stock with the listing of a rights issue.
The stock ended at 19 rupees, down 1.50 or 7.32 percent, the steepest fall for the day with over 10 million shares changing hands.
The trades generated a turnover of 193 million rupees.
Its parent firm, John Keells Holdings, closed at 190 rupees, up 75 cents.