South Africa have made three changes with regular captain Temba Bavuma ruled out of the remainder of the limited-overs series, which includes three Twenty20I matches as well, due to a broken thumb.
Bavuma was hit on the hand with a throw from a Sri Lankan fielder while returning to his crease in the team's opening loss. Maharaj will lead the side in the ODI matches.
The tourists have included batsman Reeza Hendricks, all-rounder Wiaan Mulder and debutant spinner George Linde.
Sri Lanka, led by Dasun Shanaka, have come unchanged from their 14-run win on Thursday.
The series, which holds crucial Super League points for both teams as they eye direct qualification for the 2023 50-over World Cup, is being played without spectators due to the coronavirus pandemic.
Sri Lanka: Avishka Fernando, Minod Bhanuka (wk), Bhanuka Rajapaksa, Dhananjaya de Silva, Charith Asalanka, Dasun Shanaka (capt), Wanindu Hasaranga, Chamika Karunaratne, Dushmantha Chameera, Akila Dananjaya, Praveen Jayawickram
South Africa: Janneman Malan, Aiden Markram, Reeza Hendricks, Rassie vane van der Dussen, Kyle Verreynne, Heinrich Klaasen (wk), Andile Phehlukwayo, Keshav Maharaj, Kagiso Rabada, Tabraiz Shamsi, Anrich Nortje