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He will become the 18th man to lead Sri Lanka in Test cricket.
Arthur, whose last assignment with the Sri Lankan team is a two-Test series against the West Indies beginning November 21, will move to English county side Derbyshire.
Malinga derailed England's chase after Angelo Mathews' unbeaten 85 had powered the 1996 champions to what appeared a below-par 232/9.
Sri Lanka's 20-run win over England had breathed life into their inconsistent campaign, but a painful defeat against South Africa, in the very next game, hurt their semifinals chances.
Malinga said he hoped to play T20 cricket and had his sights on the 2020 World Cup in Australia.
Karunaratne, who has no history of disciplinary problems, or his lawyer was not immediately available for comments.
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