The 32-year-old Malinga could not recover from a knee injury that he sustained during West Indies' tour of Sri Lanka in October and November and was ruled out of the series.
The two T20 Internationals will be played on January 7 in Mount Maunganui andJanuary 10 at Auckland.
Chandimal had led Sri Lanka in the T20 format till Malinga took charge in 2014.
Sri Lanka came up with a disappointing performance in the ongoing series where they lost the Tests 0-2 and are currently down 0-2 in the five-match ODI series.
Former captain Arjuna Ranatunga blamed the administrators for the defeats.
"We only developed individuals as super players, never thought about building a decent team. Selectors did a lot of mistakes with selections," said Ranatunga, the current Minister of Ports and Shipping.
Ranatunga is vying for a Vice Presidency in next week's election to appoint office bearers to SLC.
His younger brother Nishantha and the deputy speaker of parliament Thilanga Sumathipala are the main contenders for the Chairman's position.
The election is to end the SLC rule under a politically appointed interim committee who took office in April this year.