Mathews was suspended for two games for a slow over-rate offence during the Celkon Mobile Cup tri-series final against India last week in the Caribbean.
The 23-year-old Chandimal is Sri Lanka's youngest ODI captain. Lahiru Thirimanne was named as the vice-captain. The 15-man squad announced on Wednesday (July 17) also sees the return of opener Tillakaratne Dilshan.
Dilshan had missed the Celkon Mobile Cup due to an injury. Jehan Mubarak has also made a comeback.
The first ODI is on July 20 at the R Premadasa Stadium in Colombo. It is a five-match bilateral series.
Sri Lanka squad
Dinesh Chandimal (captain), Lahiru Thirimanna, Tillakaratne Dilshan, Upul Tharanga, Kumar Sangakkara, Mahela Jayawardene, Angelo Perera, Jehan Mubarak, Rangana Herath, Sachitra Senanayake, Ajantha Mendis, Lasith Malinga, Shamindra Eranga, Thisara Perera, Suranga Lakmal.