Gunathilaka, 27, was suspended on Sunday by Sri Lanka Cricket over a "misconduct" charge after a close associate of his was arrested for allegedly raping a Norwegian woman in the team hotel in Colombo.
The Sri Lanka board had said Gunathilaka, who was allegedly in the room at the same time but was not arrested, will remain suspended pending a disciplinary inquiry.
It was unclear, however, when the inquiry will begin.
His suspension is a blow to Sri Lanka as Gunathilaka was the side's second-highest-scoring batsman in the 2-0 Test series whitewash completed on Monday.
The ODI series also marks the return of Angelo Mathews to the helm, who will lead Sri Lanka against South Africa in the five-match ODI series. Mathews was reinstated as Sri Lanka's limited-overs captain in January this year, but was hit by injury less than two weeks into his new leadership stint. He had since been out of both ODIs and T20Is for Sri Lanka.
The ODI series begins on Sunday at Dambulla and ends on August 12 in Colombo. A one-off Twenty20 is due to be played in Colombo on August 14.
Angelo Mathews (Captain), Dasun Shanaka, Kusal Perera, Dhananjaya de Silva, Upul Tharanga, Kusal Mendis, Thisara Perera, Niroshan Dickwella, Suranga Lakmal, Lahiru Kumara, Kasun Rajitha, Akila Dananjaya, Prabath Jayasuriya, Lakshan Sandakan, and Shehan Jayasuriya