Malinga, feared for his awkward action and toe-crushing yorkers, returned to international cricket during June's Champions Trophy following a knee injury that kept him out of the World Twenty20 last year.
BCCI announce venues for Sri Lanka tour
But the 34-year-old has not been as effective since his comeback and has managed 10 wickets from 13 ODIs since his return.
The Galle-born pacer has taken 301 wickets from 204 matches in his career.
Sri Lanka, made a stunning return to winning ways in the first Test against Pakistan after humiliation at home against India, will also be without former captain and all-rounder Angelo Mathews in the second Test as well, who is struggling with a calf injury.
Herath stars as Pakistan crumble in first Test
The first ODI will be played on October 13 in Dubai with the teams also slated to play a three-match T20I series.
Squad:
Upul Tharanga (captain), Dinesh Chandimal, Niroshan Dickwella, Lahiru Thirimanne, Kusal Mendis, Milinda Siriwardana, Chamara Kapugedara, Thisara Perera, Seekuge Prasanna, Nuwan Pradeep, Suranga Lakmal, Dushmantha Chameera, Vishwa Fernando, Akila Dananjaya, Jeffrey Vandersay
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