Chandimal, 24, opted out of the last three matches, including the semi-final and final, of the recent World Twenty20 in Bangladesh due to poor batting form, leaving Malinga in charge.
Sri Lanka went on to beat the West Indies in the semi-final and India in the final to win their first major title since 1996 when they bagged the 50-over World Cup.
All-rounder Mathews was retained as the Test and one-day captain till the end of next year's World Cup in Australia and New Zealand, a release from Sri Lanka Cricket said.
Lahiru Thirimanne, a 24-year-old left-hand batsman, was promoted to vice-captain in all three formats, the release added.
Sri Lanka have yet to appoint a new coach after Englishman Paul Farbrace resigned on Tuesday to take up a possible assignment with England.
Farbrace, 46, has been linked to the post of assistant coach to Peter Moores, who was named England's chief coach last week replacing Zimbabwean Andy Flower.
Sri Lanka are due to play two one-day matches against