Gunathilaka will miss out due to a shoulder injury while Tharanga has been given a two-match suspension by for the slow over rate in the second ODI in Pallekele.
In a rather surprising move, Chamara Kapugedera will lead the side in Tharanga's absence.
Tharanga also sat out in two matches during the Champions Trophy.
Gunathilaka sustained a shoulder injury in the 33rd over of India's innings, when he dived to his right from point and landed heavily on his elbow.
Asanka Gurusinha, Sri Lanka's cricket manager and a selector, said the selectors wanted to stick with Kapugedera, as he was already serving as Tharanga's deputy in the series.
"The main reason for appointing Kapu as the captain is because he was actually Upul's deputy in the first two matches, and we wanted to stick with him, rather than bringing someone from outside," Gurusinha said. "We wanted someone who can hold his place in the side as well. He's also respected in the team." was quoted as saying by ESPNCricinfo.
Kapugedera has played 100 ODIs and averages 21.22 in the format with eight fifties. He has not captained Sri Lanka previously. In Pallekele, he made 40 at No. 7 adding 91 runs with Milinda Siriwardana. In the last five years, however, Kapugedera averages an11.83 over six ODI innings.
Gunathilaka's unavailability may open up an opportunity for Thirimanne, who last played an ODI for Sri Lanka in January 2016.
Neither Chandimal nor Thirimanne was part of Sri Lanka's ODI squad against Zimbabwe last month, having lost form in the format before they were dropped.
India: Rohit Sharma, Shikhar Dhawan, Virat Kohli(c), Lokesh Rahul, Kedar Jadhav, MS Dhoni(w), Manish Pandey, Axar Patel, Bhuvneshwar Kumar, Jasprit Bumrah, Yuzvendra Chahal, Ajinkya Rahane, Hardik Pandya, Shardul Thakur, Kuldeep Yadav
Sri Lanka: Niroshan Dickwella(w), Lahiru Thirimanne, Kusal Mendis, Dinesh Chandimal, Angelo Mathews, Milinda Siriwardana, Chamara Kapugedera(c), Akila Dananjaya, Dushmantha Chameera, Vishwa Fernando, Thisara Perera, Malinda Pushpakumara, Lakshan Sandakan, Wanidu Hasaranga, Lasith Malinga
First Published: August 26, 2017, 11:17 AM IST